diff -Nru gromacs-2016.2/cmake/gmxManageSimd.cmake gromacs-2016.3/cmake/gmxManageSimd.cmake
--- gromacs-2016.2/cmake/gmxManageSimd.cmake	2016-12-06 18:53:27.000000000 +0000
+++ gromacs-2016.3/cmake/gmxManageSimd.cmake	2017-03-13 17:22:33.000000000 +0000
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -74,6 +74,11 @@
             message(FATAL_ERROR "Using VSX SIMD in double precision with GCC requires GCC-4.9 or later.")
         endif()
     endif()
+    if(${CMAKE_CXX_COMPILER_ID} MATCHES "XL" OR ${CMAKE_C_COMPILER_ID} MATCHES "XL")
+        if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS "13.1.5" OR CMAKE_C_COMPILER_VERSION VERSION_LESS "13.1.5")
+            message(FATAL_ERROR "Using VSX SIMD requires XL compiler version 13.1.5 or later.")
+        endif()
+    endif()
 endmacro()
 
 # Issue a fatal error with an appropriate message, when the toolchain
@@ -418,7 +423,12 @@
         SIMD_${GMX_SIMD}_C_FLAGS SIMD_${GMX_SIMD}_CXX_FLAGS
         "-mvsx" "-maltivec -mabi=altivec" "-qarch=auto -qaltivec")
 
-    if(NOT SIMD_${GMX_SIMD}_C_FLAGS OR NOT SIMD_${GMX_SIMD}_CXX_FLAGS)
+    # Usually we check also for the C compiler here, but a C compiler
+    # is not required for SIMD support on this platform. cmake through
+    # at least version 3.7 cannot pass this check with the C compiler
+    # in the latest xlc 13.1.5, but the C++ compiler has different
+    # behaviour and is OK. See Redmine #2102.
+    if(NOT SIMD_${GMX_SIMD}_CXX_FLAGS)
         gmx_give_fatal_error_when_simd_support_not_found("IBM VSX" "disable SIMD support (slower)" "${SUGGEST_BINUTILS_UPDATE}")
     endif()
 
@@ -476,11 +486,16 @@
 # rather than actual vector data. For now we disable __vectorcall with clang
 # when using the reference build.
 # 
+# xlc 13.1.5 does not seem recognize any attribute, and warns about invalid ones
+# so we avoid searching for any.
+#
 if(NOT DEFINED GMX_SIMD_CALLING_CONVENTION)
     if(GMX_TARGET_BGQ)
         set(CALLCONV_LIST " ")
     elseif(CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND GMX_SIMD STREQUAL "REFERENCE")
         set(CALLCONV_LIST __regcall " ")
+   elseif(CMAKE_CXX_COMPILER_ID MATCHES "XL")
+        set(CALLCONV_LIST " ")
     else()
         set(CALLCONV_LIST __vectorcall __regcall " ")
     endif()
diff -Nru gromacs-2016.2/cmake/gmxVersionInfo.cmake gromacs-2016.3/cmake/gmxVersionInfo.cmake
--- gromacs-2016.2/cmake/gmxVersionInfo.cmake	2017-02-07 10:47:41.000000000 +0000
+++ gromacs-2016.3/cmake/gmxVersionInfo.cmake	2017-03-13 17:22:33.000000000 +0000
@@ -188,7 +188,7 @@
 # The GROMACS convention is that these are the version number of the next
 # release that is going to be made from this branch.
 set(GMX_VERSION_MAJOR 2016)
-set(GMX_VERSION_PATCH 2)
+set(GMX_VERSION_PATCH 3)
 # The suffix, on the other hand, is used mainly for betas and release
 # candidates, where it signifies the most recent such release from
 # this branch; it will be empty before the first such release, as well
@@ -205,7 +205,7 @@
 # code being able to dynamically link with a version of libgromacs
 # that might not work.
 set(LIBRARY_SOVERSION_MAJOR 2)
-set(LIBRARY_SOVERSION_MINOR 2)
+set(LIBRARY_SOVERSION_MINOR 3)
 set(LIBRARY_VERSION ${LIBRARY_SOVERSION_MAJOR}.${LIBRARY_SOVERSION_MINOR}.0)
 
 #####################################################################
@@ -228,7 +228,7 @@
 
 set(REGRESSIONTEST_VERSION "${GMX_VERSION_STRING}")
 set(REGRESSIONTEST_BRANCH "refs/heads/release-2016")
-set(REGRESSIONTEST_MD5SUM "e4d24e3c5f28602c2429b3a389121de8" CACHE INTERNAL "MD5 sum of the regressiontests tarball")
+set(REGRESSIONTEST_MD5SUM "bed92d1d9cdca66fbd2efa142b6e0dd3" CACHE INTERNAL "MD5 sum of the regressiontests tarball")
 
 math(EXPR GMX_VERSION_NUMERIC
      "${GMX_VERSION_MAJOR}*10000 + ${GMX_VERSION_PATCH}")
diff -Nru gromacs-2016.2/debian/changelog gromacs-2016.3/debian/changelog
--- gromacs-2016.2/debian/changelog	2017-02-09 01:58:11.000000000 +0000
+++ gromacs-2016.3/debian/changelog	2017-03-16 04:18:12.000000000 +0000
@@ -1,3 +1,9 @@
+gromacs (2016.3-1) experimental; urgency=medium
+
+  * New upstream release.
+
+ -- Nicholas Breen <nbreen@debian.org>  Wed, 15 Mar 2017 21:18:12 -0700
+
 gromacs (2016.2-1) experimental; urgency=medium
 
   * New upstream release.  Uploaded to experimental during freeze.
diff -Nru gromacs-2016.2/docs/CMakeLists.txt gromacs-2016.3/docs/CMakeLists.txt
--- gromacs-2016.2/docs/CMakeLists.txt	2016-12-06 18:53:27.000000000 +0000
+++ gromacs-2016.3/docs/CMakeLists.txt	2017-03-13 17:22:33.000000000 +0000
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -120,6 +120,7 @@
         user-guide/index.rst
         user-guide/getting-started.rst
         user-guide/flow.rst
+        user-guide/system-preparation.rst
         user-guide/cutoff-schemes.rst
         user-guide/mdrun-features.rst
         user-guide/mdrun-performance.rst
diff -Nru gromacs-2016.2/docs/dev-manual/jenkins.rst gromacs-2016.3/docs/dev-manual/jenkins.rst
--- gromacs-2016.2/docs/dev-manual/jenkins.rst	2016-12-06 18:53:27.000000000 +0000
+++ gromacs-2016.3/docs/dev-manual/jenkins.rst	2017-03-13 17:22:33.000000000 +0000
@@ -71,9 +71,18 @@
 clang static analysis
 ^^^^^^^^^^^^^^^^^^^^^
 
-The exact build sequence and the CMake configuration used is in
-:file:`admin/builds/clang-analysis.py`.  This file also specifies the clang
-version used for the analysis.
+The file :file:`admin/builds/clang-analyzer.py` specifies the exact build
+sequence and the CMake cache variables used for clang static analysis.  This
+file also specifies the clang version used for the analysis, as well as the C++
+compiler used (``clang-static-analyzer-<version>``).
+
+To run the analysis outside Jenkins, you should run both ``cmake`` and ``make``
+under ``scan-build`` command using the same CMake cache variables as in the
+build script. When you do the initial CMake configuration with ``scan-build``,
+it sets the C++ compiler to the analyzer. Note that using ``scan-build`` like
+this will also analyze C code, but Jenkins ignores C code for analysis. This
+can result in extra warnings, which can be suppressed by manually setting
+CMAKE_C_COMPILER to a value other than Clang static analyzer.
 
 cppcheck
 ^^^^^^^^
diff -Nru gromacs-2016.2/docs/install-guide/index.rst gromacs-2016.3/docs/install-guide/index.rst
--- gromacs-2016.2/docs/install-guide/index.rst	2016-12-06 18:53:27.000000000 +0000
+++ gromacs-2016.3/docs/install-guide/index.rst	2017-03-13 17:22:33.000000000 +0000
@@ -101,10 +101,12 @@
 
 You should strive to use the most recent version of your
 compiler. Minimum supported compiler versions are
+
 * GNU (gcc) 4.6
 * Intel (icc) 14
 * LLVM (clang) 3.4
 * Microsoft (MSVC) 2015
+
 Other compilers may work (Cray, Pathscale, older clang) but do
 not offer competitive performance. We recommend against PGI because
 the performance with C++ is very bad.
diff -Nru gromacs-2016.2/docs/man/gmx.1 gromacs-2016.3/docs/man/gmx.1
--- gromacs-2016.2/docs/man/gmx.1	2017-02-07 10:53:50.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx.1	2017-03-13 17:31:00.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx \- molecular dynamics simulation suite
 .
diff -Nru gromacs-2016.2/docs/man/gmx-anadock.1 gromacs-2016.3/docs/man/gmx-anadock.1
--- gromacs-2016.2/docs/man/gmx-anadock.1	2017-02-07 10:53:46.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-anadock.1	2017-03-13 17:30:55.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-ANADOCK" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-ANADOCK" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-anadock \- Cluster structures from Autodock runs
 .
diff -Nru gromacs-2016.2/docs/man/gmx-anaeig.1 gromacs-2016.3/docs/man/gmx-anaeig.1
--- gromacs-2016.2/docs/man/gmx-anaeig.1	2017-02-07 10:53:46.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-anaeig.1	2017-03-13 17:30:55.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-ANAEIG" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-ANAEIG" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-anaeig \- Analyze eigenvectors/normal modes
 .
diff -Nru gromacs-2016.2/docs/man/gmx-analyze.1 gromacs-2016.3/docs/man/gmx-analyze.1
--- gromacs-2016.2/docs/man/gmx-analyze.1	2017-02-07 10:53:46.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-analyze.1	2017-03-13 17:30:55.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-ANALYZE" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-ANALYZE" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-analyze \- Analyze data sets
 .
diff -Nru gromacs-2016.2/docs/man/gmx-angle.1 gromacs-2016.3/docs/man/gmx-angle.1
--- gromacs-2016.2/docs/man/gmx-angle.1	2017-02-07 10:53:46.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-angle.1	2017-03-13 17:30:55.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-ANGLE" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-ANGLE" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-angle \- Calculate distributions and correlations for angles and dihedrals
 .
diff -Nru gromacs-2016.2/docs/man/gmx-bar.1 gromacs-2016.3/docs/man/gmx-bar.1
--- gromacs-2016.2/docs/man/gmx-bar.1	2017-02-07 10:53:46.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-bar.1	2017-03-13 17:30:55.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-BAR" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-BAR" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-bar \- Calculate free energy difference estimates through Bennett's acceptance ratio
 .
diff -Nru gromacs-2016.2/docs/man/gmx-bundle.1 gromacs-2016.3/docs/man/gmx-bundle.1
--- gromacs-2016.2/docs/man/gmx-bundle.1	2017-02-07 10:53:46.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-bundle.1	2017-03-13 17:30:55.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-BUNDLE" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-BUNDLE" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-bundle \- Analyze bundles of axes, e.g., helices
 .
diff -Nru gromacs-2016.2/docs/man/gmx-check.1 gromacs-2016.3/docs/man/gmx-check.1
--- gromacs-2016.2/docs/man/gmx-check.1	2017-02-07 10:53:46.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-check.1	2017-03-13 17:30:55.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-CHECK" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-CHECK" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-check \- Check and compare files
 .
diff -Nru gromacs-2016.2/docs/man/gmx-chi.1 gromacs-2016.3/docs/man/gmx-chi.1
--- gromacs-2016.2/docs/man/gmx-chi.1	2017-02-07 10:53:46.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-chi.1	2017-03-13 17:30:55.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-CHI" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-CHI" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-chi \- Calculate everything you want to know about chi and other dihedrals
 .
diff -Nru gromacs-2016.2/docs/man/gmx-cluster.1 gromacs-2016.3/docs/man/gmx-cluster.1
--- gromacs-2016.2/docs/man/gmx-cluster.1	2017-02-07 10:53:46.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-cluster.1	2017-03-13 17:30:55.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-CLUSTER" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-CLUSTER" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-cluster \- Cluster structures
 .
diff -Nru gromacs-2016.2/docs/man/gmx-clustsize.1 gromacs-2016.3/docs/man/gmx-clustsize.1
--- gromacs-2016.2/docs/man/gmx-clustsize.1	2017-02-07 10:53:46.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-clustsize.1	2017-03-13 17:30:55.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-CLUSTSIZE" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-CLUSTSIZE" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-clustsize \- Calculate size distributions of atomic clusters
 .
diff -Nru gromacs-2016.2/docs/man/gmx-confrms.1 gromacs-2016.3/docs/man/gmx-confrms.1
--- gromacs-2016.2/docs/man/gmx-confrms.1	2017-02-07 10:53:46.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-confrms.1	2017-03-13 17:30:55.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-CONFRMS" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-CONFRMS" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-confrms \- Fit two structures and calculates the RMSD
 .
diff -Nru gromacs-2016.2/docs/man/gmx-convert-tpr.1 gromacs-2016.3/docs/man/gmx-convert-tpr.1
--- gromacs-2016.2/docs/man/gmx-convert-tpr.1	2017-02-07 10:53:46.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-convert-tpr.1	2017-03-13 17:30:55.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-CONVERT-TPR" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-CONVERT-TPR" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-convert-tpr \- Make a modifed run-input file
 .
diff -Nru gromacs-2016.2/docs/man/gmx-covar.1 gromacs-2016.3/docs/man/gmx-covar.1
--- gromacs-2016.2/docs/man/gmx-covar.1	2017-02-07 10:53:46.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-covar.1	2017-03-13 17:30:55.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-COVAR" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-COVAR" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-covar \- Calculate and diagonalize the covariance matrix
 .
diff -Nru gromacs-2016.2/docs/man/gmx-current.1 gromacs-2016.3/docs/man/gmx-current.1
--- gromacs-2016.2/docs/man/gmx-current.1	2017-02-07 10:53:46.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-current.1	2017-03-13 17:30:55.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-CURRENT" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-CURRENT" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-current \- Calculate dielectric constants and current autocorrelation function
 .
diff -Nru gromacs-2016.2/docs/man/gmx-density.1 gromacs-2016.3/docs/man/gmx-density.1
--- gromacs-2016.2/docs/man/gmx-density.1	2017-02-07 10:53:46.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-density.1	2017-03-13 17:30:56.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-DENSITY" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-DENSITY" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-density \- Calculate the density of the system
 .
diff -Nru gromacs-2016.2/docs/man/gmx-densmap.1 gromacs-2016.3/docs/man/gmx-densmap.1
--- gromacs-2016.2/docs/man/gmx-densmap.1	2017-02-07 10:53:46.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-densmap.1	2017-03-13 17:30:56.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-DENSMAP" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-DENSMAP" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-densmap \- Calculate 2D planar or axial-radial density maps
 .
diff -Nru gromacs-2016.2/docs/man/gmx-densorder.1 gromacs-2016.3/docs/man/gmx-densorder.1
--- gromacs-2016.2/docs/man/gmx-densorder.1	2017-02-07 10:53:46.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-densorder.1	2017-03-13 17:30:56.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-DENSORDER" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-DENSORDER" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-densorder \- Calculate surface fluctuations
 .
diff -Nru gromacs-2016.2/docs/man/gmx-dielectric.1 gromacs-2016.3/docs/man/gmx-dielectric.1
--- gromacs-2016.2/docs/man/gmx-dielectric.1	2017-02-07 10:53:47.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-dielectric.1	2017-03-13 17:30:56.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-DIELECTRIC" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-DIELECTRIC" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-dielectric \- Calculate frequency dependent dielectric constants
 .
diff -Nru gromacs-2016.2/docs/man/gmx-dipoles.1 gromacs-2016.3/docs/man/gmx-dipoles.1
--- gromacs-2016.2/docs/man/gmx-dipoles.1	2017-02-07 10:53:47.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-dipoles.1	2017-03-13 17:30:56.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-DIPOLES" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-DIPOLES" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-dipoles \- Compute the total dipole plus fluctuations
 .
diff -Nru gromacs-2016.2/docs/man/gmx-disre.1 gromacs-2016.3/docs/man/gmx-disre.1
--- gromacs-2016.2/docs/man/gmx-disre.1	2017-02-07 10:53:47.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-disre.1	2017-03-13 17:30:56.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-DISRE" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-DISRE" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-disre \- Analyze distance restraints
 .
diff -Nru gromacs-2016.2/docs/man/gmx-distance.1 gromacs-2016.3/docs/man/gmx-distance.1
--- gromacs-2016.2/docs/man/gmx-distance.1	2017-02-07 10:53:47.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-distance.1	2017-03-13 17:30:56.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-DISTANCE" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-DISTANCE" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-distance \- Calculate distances between pairs of positions
 .
diff -Nru gromacs-2016.2/docs/man/gmx-do_dssp.1 gromacs-2016.3/docs/man/gmx-do_dssp.1
--- gromacs-2016.2/docs/man/gmx-do_dssp.1	2017-02-07 10:53:47.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-do_dssp.1	2017-03-13 17:30:56.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-DO_DSSP" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-DO_DSSP" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-do_dssp \- Assign secondary structure and calculate solvent accessible surface area
 .
diff -Nru gromacs-2016.2/docs/man/gmx-dos.1 gromacs-2016.3/docs/man/gmx-dos.1
--- gromacs-2016.2/docs/man/gmx-dos.1	2017-02-07 10:53:47.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-dos.1	2017-03-13 17:30:56.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-DOS" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-DOS" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-dos \- Analyze density of states and properties based on that
 .
diff -Nru gromacs-2016.2/docs/man/gmx-dump.1 gromacs-2016.3/docs/man/gmx-dump.1
--- gromacs-2016.2/docs/man/gmx-dump.1	2017-02-07 10:53:47.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-dump.1	2017-03-13 17:30:56.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-DUMP" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-DUMP" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-dump \- Make binary files human readable
 .
diff -Nru gromacs-2016.2/docs/man/gmx-dyecoupl.1 gromacs-2016.3/docs/man/gmx-dyecoupl.1
--- gromacs-2016.2/docs/man/gmx-dyecoupl.1	2017-02-07 10:53:47.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-dyecoupl.1	2017-03-13 17:30:56.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-DYECOUPL" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-DYECOUPL" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-dyecoupl \- Extract dye dynamics from trajectories
 .
diff -Nru gromacs-2016.2/docs/man/gmx-dyndom.1 gromacs-2016.3/docs/man/gmx-dyndom.1
--- gromacs-2016.2/docs/man/gmx-dyndom.1	2017-02-07 10:53:47.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-dyndom.1	2017-03-13 17:30:56.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-DYNDOM" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-DYNDOM" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-dyndom \- Interpolate and extrapolate structure rotations
 .
diff -Nru gromacs-2016.2/docs/man/gmx-editconf.1 gromacs-2016.3/docs/man/gmx-editconf.1
--- gromacs-2016.2/docs/man/gmx-editconf.1	2017-02-07 10:53:47.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-editconf.1	2017-03-13 17:30:56.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-EDITCONF" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-EDITCONF" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-editconf \- Convert and manipulates structure files
 .
diff -Nru gromacs-2016.2/docs/man/gmx-eneconv.1 gromacs-2016.3/docs/man/gmx-eneconv.1
--- gromacs-2016.2/docs/man/gmx-eneconv.1	2017-02-07 10:53:47.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-eneconv.1	2017-03-13 17:30:56.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-ENECONV" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-ENECONV" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-eneconv \- Convert energy files
 .
diff -Nru gromacs-2016.2/docs/man/gmx-enemat.1 gromacs-2016.3/docs/man/gmx-enemat.1
--- gromacs-2016.2/docs/man/gmx-enemat.1	2017-02-07 10:53:47.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-enemat.1	2017-03-13 17:30:56.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-ENEMAT" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-ENEMAT" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-enemat \- Extract an energy matrix from an energy file
 .
diff -Nru gromacs-2016.2/docs/man/gmx-energy.1 gromacs-2016.3/docs/man/gmx-energy.1
--- gromacs-2016.2/docs/man/gmx-energy.1	2017-02-07 10:53:47.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-energy.1	2017-03-13 17:30:56.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-ENERGY" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-ENERGY" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-energy \- Writes energies to xvg files and display averages
 .
diff -Nru gromacs-2016.2/docs/man/gmx-filter.1 gromacs-2016.3/docs/man/gmx-filter.1
--- gromacs-2016.2/docs/man/gmx-filter.1	2017-02-07 10:53:47.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-filter.1	2017-03-13 17:30:57.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-FILTER" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-FILTER" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-filter \- Frequency filter trajectories, useful for making smooth movies
 .
diff -Nru gromacs-2016.2/docs/man/gmx-freevolume.1 gromacs-2016.3/docs/man/gmx-freevolume.1
--- gromacs-2016.2/docs/man/gmx-freevolume.1	2017-02-07 10:53:47.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-freevolume.1	2017-03-13 17:30:57.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-FREEVOLUME" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-FREEVOLUME" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-freevolume \- Calculate free volume
 .
diff -Nru gromacs-2016.2/docs/man/gmx-gangle.1 gromacs-2016.3/docs/man/gmx-gangle.1
--- gromacs-2016.2/docs/man/gmx-gangle.1	2017-02-07 10:53:47.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-gangle.1	2017-03-13 17:30:57.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-GANGLE" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-GANGLE" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-gangle \- Calculate angles
 .
diff -Nru gromacs-2016.2/docs/man/gmx-genconf.1 gromacs-2016.3/docs/man/gmx-genconf.1
--- gromacs-2016.2/docs/man/gmx-genconf.1	2017-02-07 10:53:47.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-genconf.1	2017-03-13 17:30:57.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-GENCONF" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-GENCONF" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-genconf \- Multiply a conformation in 'random' orientations
 .
diff -Nru gromacs-2016.2/docs/man/gmx-genion.1 gromacs-2016.3/docs/man/gmx-genion.1
--- gromacs-2016.2/docs/man/gmx-genion.1	2017-02-07 10:53:47.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-genion.1	2017-03-13 17:30:57.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-GENION" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-GENION" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-genion \- Generate monoatomic ions on energetically favorable positions
 .
diff -Nru gromacs-2016.2/docs/man/gmx-genrestr.1 gromacs-2016.3/docs/man/gmx-genrestr.1
--- gromacs-2016.2/docs/man/gmx-genrestr.1	2017-02-07 10:53:47.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-genrestr.1	2017-03-13 17:30:57.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-GENRESTR" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-GENRESTR" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-genrestr \- Generate position restraints or distance restraints for index groups
 .
diff -Nru gromacs-2016.2/docs/man/gmx-grompp.1 gromacs-2016.3/docs/man/gmx-grompp.1
--- gromacs-2016.2/docs/man/gmx-grompp.1	2017-02-07 10:53:47.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-grompp.1	2017-03-13 17:30:57.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-GROMPP" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-GROMPP" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-grompp \- Make a run input file
 .
diff -Nru gromacs-2016.2/docs/man/gmx-gyrate.1 gromacs-2016.3/docs/man/gmx-gyrate.1
--- gromacs-2016.2/docs/man/gmx-gyrate.1	2017-02-07 10:53:47.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-gyrate.1	2017-03-13 17:30:57.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-GYRATE" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-GYRATE" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-gyrate \- Calculate the radius of gyration
 .
diff -Nru gromacs-2016.2/docs/man/gmx-h2order.1 gromacs-2016.3/docs/man/gmx-h2order.1
--- gromacs-2016.2/docs/man/gmx-h2order.1	2017-02-07 10:53:47.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-h2order.1	2017-03-13 17:30:57.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-H2ORDER" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-H2ORDER" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-h2order \- Compute the orientation of water molecules
 .
diff -Nru gromacs-2016.2/docs/man/gmx-hbond.1 gromacs-2016.3/docs/man/gmx-hbond.1
--- gromacs-2016.2/docs/man/gmx-hbond.1	2017-02-07 10:53:47.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-hbond.1	2017-03-13 17:30:57.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-HBOND" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-HBOND" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-hbond \- Compute and analyze hydrogen bonds
 .
diff -Nru gromacs-2016.2/docs/man/gmx-helix.1 gromacs-2016.3/docs/man/gmx-helix.1
--- gromacs-2016.2/docs/man/gmx-helix.1	2017-02-07 10:53:47.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-helix.1	2017-03-13 17:30:57.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-HELIX" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-HELIX" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-helix \- Calculate basic properties of alpha helices
 .
diff -Nru gromacs-2016.2/docs/man/gmx-helixorient.1 gromacs-2016.3/docs/man/gmx-helixorient.1
--- gromacs-2016.2/docs/man/gmx-helixorient.1	2017-02-07 10:53:47.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-helixorient.1	2017-03-13 17:30:57.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-HELIXORIENT" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-HELIXORIENT" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-helixorient \- Calculate local pitch/bending/rotation/orientation inside helices
 .
diff -Nru gromacs-2016.2/docs/man/gmx-help.1 gromacs-2016.3/docs/man/gmx-help.1
--- gromacs-2016.2/docs/man/gmx-help.1	2017-02-07 10:53:47.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-help.1	2017-03-13 17:30:57.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-HELP" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-HELP" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-help \- Print help information
 .
diff -Nru gromacs-2016.2/docs/man/gmx-hydorder.1 gromacs-2016.3/docs/man/gmx-hydorder.1
--- gromacs-2016.2/docs/man/gmx-hydorder.1	2017-02-07 10:53:48.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-hydorder.1	2017-03-13 17:30:57.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-HYDORDER" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-HYDORDER" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-hydorder \- Compute tetrahedrality parameters around a given atom
 .
diff -Nru gromacs-2016.2/docs/man/gmx-insert-molecules.1 gromacs-2016.3/docs/man/gmx-insert-molecules.1
--- gromacs-2016.2/docs/man/gmx-insert-molecules.1	2017-02-07 10:53:48.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-insert-molecules.1	2017-03-13 17:30:57.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-INSERT-MOLECULES" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-INSERT-MOLECULES" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-insert-molecules \- Insert molecules into existing vacancies
 .
@@ -71,7 +71,10 @@
 inserted molecule is less than the sum based on the van der Waals
 radii of both atoms. A database (\fBvdwradii.dat\fP) of van der
 Waals radii is read by the program, and the resulting radii scaled
-by \fB\-scale\fP\&. If radii are not found in the database, thoseatoms are assigned the (pre\-scaled) distance \fB\-radius\fP\&.
+by \fB\-scale\fP\&. If radii are not found in the database, those
+atoms are assigned the (pre\-scaled) distance \fB\-radius\fP\&.
+Note that the usefulness of those radii depends on the atom names,
+and thus varies widely with force field.
 .sp
 A total of \fB\-nmol\fP * \fB\-try\fP insertion attempts are made
 before giving up. Increase \fB\-try\fP if you have several small
diff -Nru gromacs-2016.2/docs/man/gmx-lie.1 gromacs-2016.3/docs/man/gmx-lie.1
--- gromacs-2016.2/docs/man/gmx-lie.1	2017-02-07 10:53:48.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-lie.1	2017-03-13 17:30:57.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-LIE" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-LIE" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-lie \- Estimate free energy from linear combinations
 .
diff -Nru gromacs-2016.2/docs/man/gmx-make_edi.1 gromacs-2016.3/docs/man/gmx-make_edi.1
--- gromacs-2016.2/docs/man/gmx-make_edi.1	2017-02-07 10:53:48.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-make_edi.1	2017-03-13 17:30:57.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-MAKE_EDI" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-MAKE_EDI" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-make_edi \- Generate input files for essential dynamics sampling
 .
diff -Nru gromacs-2016.2/docs/man/gmx-make_ndx.1 gromacs-2016.3/docs/man/gmx-make_ndx.1
--- gromacs-2016.2/docs/man/gmx-make_ndx.1	2017-02-07 10:53:48.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-make_ndx.1	2017-03-13 17:30:57.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-MAKE_NDX" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-MAKE_NDX" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-make_ndx \- Make index files
 .
diff -Nru gromacs-2016.2/docs/man/gmx-mdmat.1 gromacs-2016.3/docs/man/gmx-mdmat.1
--- gromacs-2016.2/docs/man/gmx-mdmat.1	2017-02-07 10:53:48.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-mdmat.1	2017-03-13 17:30:58.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-MDMAT" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-MDMAT" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-mdmat \- Calculate residue contact maps
 .
diff -Nru gromacs-2016.2/docs/man/gmx-mdrun.1 gromacs-2016.3/docs/man/gmx-mdrun.1
--- gromacs-2016.2/docs/man/gmx-mdrun.1	2017-02-07 10:53:48.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-mdrun.1	2017-03-13 17:30:58.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-MDRUN" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-MDRUN" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-mdrun \- Perform a simulation, do a normal mode analysis or an energy minimization
 .
diff -Nru gromacs-2016.2/docs/man/gmx-mindist.1 gromacs-2016.3/docs/man/gmx-mindist.1
--- gromacs-2016.2/docs/man/gmx-mindist.1	2017-02-07 10:53:48.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-mindist.1	2017-03-13 17:30:58.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-MINDIST" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-MINDIST" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-mindist \- Calculate the minimum distance between two groups
 .
diff -Nru gromacs-2016.2/docs/man/gmx-mk_angndx.1 gromacs-2016.3/docs/man/gmx-mk_angndx.1
--- gromacs-2016.2/docs/man/gmx-mk_angndx.1	2017-02-07 10:53:48.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-mk_angndx.1	2017-03-13 17:30:58.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-MK_ANGNDX" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-MK_ANGNDX" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-mk_angndx \- Generate index files for 'gmx angle'
 .
diff -Nru gromacs-2016.2/docs/man/gmx-morph.1 gromacs-2016.3/docs/man/gmx-morph.1
--- gromacs-2016.2/docs/man/gmx-morph.1	2017-02-07 10:53:48.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-morph.1	2017-03-13 17:30:58.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-MORPH" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-MORPH" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-morph \- Interpolate linearly between conformations
 .
diff -Nru gromacs-2016.2/docs/man/gmx-msd.1 gromacs-2016.3/docs/man/gmx-msd.1
--- gromacs-2016.2/docs/man/gmx-msd.1	2017-02-07 10:53:48.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-msd.1	2017-03-13 17:30:58.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-MSD" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-MSD" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-msd \- Calculates mean square displacements
 .
diff -Nru gromacs-2016.2/docs/man/gmx-nmeig.1 gromacs-2016.3/docs/man/gmx-nmeig.1
--- gromacs-2016.2/docs/man/gmx-nmeig.1	2017-02-07 10:53:48.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-nmeig.1	2017-03-13 17:30:58.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-NMEIG" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-NMEIG" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-nmeig \- Diagonalize the Hessian for normal mode analysis
 .
diff -Nru gromacs-2016.2/docs/man/gmx-nmens.1 gromacs-2016.3/docs/man/gmx-nmens.1
--- gromacs-2016.2/docs/man/gmx-nmens.1	2017-02-07 10:53:48.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-nmens.1	2017-03-13 17:30:58.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-NMENS" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-NMENS" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-nmens \- Generate an ensemble of structures from the normal modes
 .
diff -Nru gromacs-2016.2/docs/man/gmx-nmtraj.1 gromacs-2016.3/docs/man/gmx-nmtraj.1
--- gromacs-2016.2/docs/man/gmx-nmtraj.1	2017-02-07 10:53:48.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-nmtraj.1	2017-03-13 17:30:58.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-NMTRAJ" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-NMTRAJ" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-nmtraj \- Generate a virtual oscillating trajectory from an eigenvector
 .
diff -Nru gromacs-2016.2/docs/man/gmx-order.1 gromacs-2016.3/docs/man/gmx-order.1
--- gromacs-2016.2/docs/man/gmx-order.1	2017-02-07 10:53:48.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-order.1	2017-03-13 17:30:58.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-ORDER" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-ORDER" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-order \- Compute the order parameter per atom for carbon tails
 .
diff -Nru gromacs-2016.2/docs/man/gmx-pairdist.1 gromacs-2016.3/docs/man/gmx-pairdist.1
--- gromacs-2016.2/docs/man/gmx-pairdist.1	2017-02-07 10:53:48.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-pairdist.1	2017-03-13 17:30:58.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-PAIRDIST" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-PAIRDIST" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-pairdist \- Calculate pairwise distances between groups of positions
 .
diff -Nru gromacs-2016.2/docs/man/gmx-pdb2gmx.1 gromacs-2016.3/docs/man/gmx-pdb2gmx.1
--- gromacs-2016.2/docs/man/gmx-pdb2gmx.1	2017-02-07 10:53:48.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-pdb2gmx.1	2017-03-13 17:30:58.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-PDB2GMX" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-PDB2GMX" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-pdb2gmx \- Convert coordinate files to topology and FF-compliant coordinate files
 .
diff -Nru gromacs-2016.2/docs/man/gmx-pme_error.1 gromacs-2016.3/docs/man/gmx-pme_error.1
--- gromacs-2016.2/docs/man/gmx-pme_error.1	2017-02-07 10:53:48.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-pme_error.1	2017-03-13 17:30:58.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-PME_ERROR" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-PME_ERROR" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-pme_error \- Estimate the error of using PME with a given input file
 .
diff -Nru gromacs-2016.2/docs/man/gmx-polystat.1 gromacs-2016.3/docs/man/gmx-polystat.1
--- gromacs-2016.2/docs/man/gmx-polystat.1	2017-02-07 10:53:48.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-polystat.1	2017-03-13 17:30:58.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-POLYSTAT" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-POLYSTAT" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-polystat \- Calculate static properties of polymers
 .
diff -Nru gromacs-2016.2/docs/man/gmx-potential.1 gromacs-2016.3/docs/man/gmx-potential.1
--- gromacs-2016.2/docs/man/gmx-potential.1	2017-02-07 10:53:48.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-potential.1	2017-03-13 17:30:58.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-POTENTIAL" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-POTENTIAL" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-potential \- Calculate the electrostatic potential across the box
 .
diff -Nru gromacs-2016.2/docs/man/gmx-principal.1 gromacs-2016.3/docs/man/gmx-principal.1
--- gromacs-2016.2/docs/man/gmx-principal.1	2017-02-07 10:53:48.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-principal.1	2017-03-13 17:30:58.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-PRINCIPAL" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-PRINCIPAL" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-principal \- Calculate principal axes of inertia for a group of atoms
 .
diff -Nru gromacs-2016.2/docs/man/gmx-rama.1 gromacs-2016.3/docs/man/gmx-rama.1
--- gromacs-2016.2/docs/man/gmx-rama.1	2017-02-07 10:53:48.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-rama.1	2017-03-13 17:30:58.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-RAMA" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-RAMA" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-rama \- Compute Ramachandran plots
 .
diff -Nru gromacs-2016.2/docs/man/gmx-rdf.1 gromacs-2016.3/docs/man/gmx-rdf.1
--- gromacs-2016.2/docs/man/gmx-rdf.1	2017-02-07 10:53:48.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-rdf.1	2017-03-13 17:30:58.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-RDF" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-RDF" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-rdf \- Calculate radial distribution functions
 .
diff -Nru gromacs-2016.2/docs/man/gmx-rms.1 gromacs-2016.3/docs/man/gmx-rms.1
--- gromacs-2016.2/docs/man/gmx-rms.1	2017-02-07 10:53:48.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-rms.1	2017-03-13 17:30:58.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-RMS" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-RMS" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-rms \- Calculate RMSDs with a reference structure and RMSD matrices
 .
diff -Nru gromacs-2016.2/docs/man/gmx-rmsdist.1 gromacs-2016.3/docs/man/gmx-rmsdist.1
--- gromacs-2016.2/docs/man/gmx-rmsdist.1	2017-02-07 10:53:48.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-rmsdist.1	2017-03-13 17:30:58.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-RMSDIST" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-RMSDIST" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-rmsdist \- Calculate atom pair distances averaged with power -2, -3 or -6
 .
diff -Nru gromacs-2016.2/docs/man/gmx-rmsf.1 gromacs-2016.3/docs/man/gmx-rmsf.1
--- gromacs-2016.2/docs/man/gmx-rmsf.1	2017-02-07 10:53:49.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-rmsf.1	2017-03-13 17:30:58.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-RMSF" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-RMSF" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-rmsf \- Calculate atomic fluctuations
 .
diff -Nru gromacs-2016.2/docs/man/gmx-rotacf.1 gromacs-2016.3/docs/man/gmx-rotacf.1
--- gromacs-2016.2/docs/man/gmx-rotacf.1	2017-02-07 10:53:49.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-rotacf.1	2017-03-13 17:30:58.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-ROTACF" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-ROTACF" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-rotacf \- Calculate the rotational correlation function for molecules
 .
diff -Nru gromacs-2016.2/docs/man/gmx-rotmat.1 gromacs-2016.3/docs/man/gmx-rotmat.1
--- gromacs-2016.2/docs/man/gmx-rotmat.1	2017-02-07 10:53:49.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-rotmat.1	2017-03-13 17:30:59.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-ROTMAT" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-ROTMAT" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-rotmat \- Plot the rotation matrix for fitting to a reference structure
 .
diff -Nru gromacs-2016.2/docs/man/gmx-saltbr.1 gromacs-2016.3/docs/man/gmx-saltbr.1
--- gromacs-2016.2/docs/man/gmx-saltbr.1	2017-02-07 10:53:49.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-saltbr.1	2017-03-13 17:30:59.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-SALTBR" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-SALTBR" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-saltbr \- Compute salt bridges
 .
diff -Nru gromacs-2016.2/docs/man/gmx-sans.1 gromacs-2016.3/docs/man/gmx-sans.1
--- gromacs-2016.2/docs/man/gmx-sans.1	2017-02-07 10:53:49.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-sans.1	2017-03-13 17:30:59.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-SANS" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-SANS" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-sans \- Compute small angle neutron scattering spectra
 .
diff -Nru gromacs-2016.2/docs/man/gmx-sasa.1 gromacs-2016.3/docs/man/gmx-sasa.1
--- gromacs-2016.2/docs/man/gmx-sasa.1	2017-02-07 10:53:49.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-sasa.1	2017-03-13 17:30:59.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-SASA" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-SASA" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-sasa \- Compute solvent accessible surface area
 .
diff -Nru gromacs-2016.2/docs/man/gmx-saxs.1 gromacs-2016.3/docs/man/gmx-saxs.1
--- gromacs-2016.2/docs/man/gmx-saxs.1	2017-02-07 10:53:49.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-saxs.1	2017-03-13 17:30:59.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-SAXS" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-SAXS" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-saxs \- Compute small angle X-ray scattering spectra
 .
diff -Nru gromacs-2016.2/docs/man/gmx-select.1 gromacs-2016.3/docs/man/gmx-select.1
--- gromacs-2016.2/docs/man/gmx-select.1	2017-02-07 10:53:49.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-select.1	2017-03-13 17:30:59.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-SELECT" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-SELECT" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-select \- Print general information about selections
 .
diff -Nru gromacs-2016.2/docs/man/gmx-sham.1 gromacs-2016.3/docs/man/gmx-sham.1
--- gromacs-2016.2/docs/man/gmx-sham.1	2017-02-07 10:53:49.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-sham.1	2017-03-13 17:30:59.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-SHAM" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-SHAM" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-sham \- Compute free energies or other histograms from histograms
 .
diff -Nru gromacs-2016.2/docs/man/gmx-sigeps.1 gromacs-2016.3/docs/man/gmx-sigeps.1
--- gromacs-2016.2/docs/man/gmx-sigeps.1	2017-02-07 10:53:49.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-sigeps.1	2017-03-13 17:30:59.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-SIGEPS" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-SIGEPS" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-sigeps \- Convert c6/12 or c6/cn combinations to and from sigma/epsilon
 .
diff -Nru gromacs-2016.2/docs/man/gmx-solvate.1 gromacs-2016.3/docs/man/gmx-solvate.1
--- gromacs-2016.2/docs/man/gmx-solvate.1	2017-02-07 10:53:49.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-solvate.1	2017-03-13 17:30:59.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-SOLVATE" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-SOLVATE" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-solvate \- Solvate a system
 .
@@ -64,7 +64,10 @@
 the solvent molecule is less than the sum of the scaled van der Waals
 radii of both atoms. A database (\fBvdwradii.dat\fP) of van der
 Waals radii is read by the program, and the resulting radii scaled
-by \fB\-scale\fP\&. If radii are not found in the database, thoseatoms are assigned the (pre\-scaled) distance \fB\-radius\fP\&.
+by \fB\-scale\fP\&. If radii are not found in the database, those
+atoms are assigned the (pre\-scaled) distance \fB\-radius\fP\&.
+Note that the usefulness of those radii depends on the atom names,
+and thus varies widely with force field.
 .sp
 The default solvent is Simple Point Charge water (SPC), with coordinates
 from \fB$GMXLIB/spc216.gro\fP\&. These coordinates can also be used
diff -Nru gromacs-2016.2/docs/man/gmx-sorient.1 gromacs-2016.3/docs/man/gmx-sorient.1
--- gromacs-2016.2/docs/man/gmx-sorient.1	2017-02-07 10:53:49.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-sorient.1	2017-03-13 17:30:59.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-SORIENT" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-SORIENT" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-sorient \- Analyze solvent orientation around solutes
 .
diff -Nru gromacs-2016.2/docs/man/gmx-spatial.1 gromacs-2016.3/docs/man/gmx-spatial.1
--- gromacs-2016.2/docs/man/gmx-spatial.1	2017-02-07 10:53:49.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-spatial.1	2017-03-13 17:30:59.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-SPATIAL" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-SPATIAL" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-spatial \- Calculate the spatial distribution function
 .
diff -Nru gromacs-2016.2/docs/man/gmx-spol.1 gromacs-2016.3/docs/man/gmx-spol.1
--- gromacs-2016.2/docs/man/gmx-spol.1	2017-02-07 10:53:49.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-spol.1	2017-03-13 17:30:59.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-SPOL" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-SPOL" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-spol \- Analyze solvent dipole orientation and polarization around solutes
 .
diff -Nru gromacs-2016.2/docs/man/gmx-tcaf.1 gromacs-2016.3/docs/man/gmx-tcaf.1
--- gromacs-2016.2/docs/man/gmx-tcaf.1	2017-02-07 10:53:49.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-tcaf.1	2017-03-13 17:30:59.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-TCAF" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-TCAF" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-tcaf \- Calculate viscosities of liquids
 .
diff -Nru gromacs-2016.2/docs/man/gmx-traj.1 gromacs-2016.3/docs/man/gmx-traj.1
--- gromacs-2016.2/docs/man/gmx-traj.1	2017-02-07 10:53:49.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-traj.1	2017-03-13 17:30:59.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-TRAJ" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-TRAJ" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-traj \- Plot x, v, f, box, temperature and rotational energy from trajectories
 .
diff -Nru gromacs-2016.2/docs/man/gmx-trjcat.1 gromacs-2016.3/docs/man/gmx-trjcat.1
--- gromacs-2016.2/docs/man/gmx-trjcat.1	2017-02-07 10:53:49.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-trjcat.1	2017-03-13 17:30:59.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-TRJCAT" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-TRJCAT" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-trjcat \- Concatenate trajectory files
 .
diff -Nru gromacs-2016.2/docs/man/gmx-trjconv.1 gromacs-2016.3/docs/man/gmx-trjconv.1
--- gromacs-2016.2/docs/man/gmx-trjconv.1	2017-02-07 10:53:49.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-trjconv.1	2017-03-13 17:30:59.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-TRJCONV" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-TRJCONV" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-trjconv \- Convert and manipulates trajectory files
 .
@@ -150,10 +150,6 @@
 results if you in fact have a cluster. Luckily that can be checked
 afterwards using a trajectory viewer. Note also that if your molecules
 are broken this will not work either.
-.sp
-The separate option \fB\-clustercenter\fP can be used to specify an
-approximate center for the cluster. This is useful e.g. if you have
-two big vesicles, and you want to maintain their relative positions.
 .IP \(bu 2
 \fBwhole\fP only makes broken molecules whole.
 .UNINDENT
diff -Nru gromacs-2016.2/docs/man/gmx-trjorder.1 gromacs-2016.3/docs/man/gmx-trjorder.1
--- gromacs-2016.2/docs/man/gmx-trjorder.1	2017-02-07 10:53:49.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-trjorder.1	2017-03-13 17:30:59.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-TRJORDER" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-TRJORDER" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-trjorder \- Order molecules according to their distance to a group
 .
diff -Nru gromacs-2016.2/docs/man/gmx-tune_pme.1 gromacs-2016.3/docs/man/gmx-tune_pme.1
--- gromacs-2016.2/docs/man/gmx-tune_pme.1	2017-02-07 10:53:49.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-tune_pme.1	2017-03-13 17:30:59.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-TUNE_PME" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-TUNE_PME" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-tune_pme \- Time mdrun as a function of PME ranks to optimize settings
 .
diff -Nru gromacs-2016.2/docs/man/gmx-vanhove.1 gromacs-2016.3/docs/man/gmx-vanhove.1
--- gromacs-2016.2/docs/man/gmx-vanhove.1	2017-02-07 10:53:49.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-vanhove.1	2017-03-13 17:30:59.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-VANHOVE" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-VANHOVE" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-vanhove \- Compute Van Hove displacement and correlation functions
 .
diff -Nru gromacs-2016.2/docs/man/gmx-velacc.1 gromacs-2016.3/docs/man/gmx-velacc.1
--- gromacs-2016.2/docs/man/gmx-velacc.1	2017-02-07 10:53:49.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-velacc.1	2017-03-13 17:31:00.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-VELACC" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-VELACC" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-velacc \- Calculate velocity autocorrelation functions
 .
diff -Nru gromacs-2016.2/docs/man/gmx-view.1 gromacs-2016.3/docs/man/gmx-view.1
--- gromacs-2016.2/docs/man/gmx-view.1	2017-02-07 10:53:49.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-view.1	2017-03-13 17:31:00.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-VIEW" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-VIEW" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-view \- View a trajectory on an X-Windows terminal
 .
diff -Nru gromacs-2016.2/docs/man/gmx-wham.1 gromacs-2016.3/docs/man/gmx-wham.1
--- gromacs-2016.2/docs/man/gmx-wham.1	2017-02-07 10:53:49.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-wham.1	2017-03-13 17:31:00.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-WHAM" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-WHAM" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-wham \- Perform weighted histogram analysis after umbrella sampling
 .
diff -Nru gromacs-2016.2/docs/man/gmx-wheel.1 gromacs-2016.3/docs/man/gmx-wheel.1
--- gromacs-2016.2/docs/man/gmx-wheel.1	2017-02-07 10:53:49.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-wheel.1	2017-03-13 17:31:00.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-WHEEL" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-WHEEL" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-wheel \- Plot helical wheels
 .
diff -Nru gromacs-2016.2/docs/man/gmx-x2top.1 gromacs-2016.3/docs/man/gmx-x2top.1
--- gromacs-2016.2/docs/man/gmx-x2top.1	2017-02-07 10:53:50.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-x2top.1	2017-03-13 17:31:00.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-X2TOP" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-X2TOP" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-x2top \- Generate a primitive topology from coordinates
 .
diff -Nru gromacs-2016.2/docs/man/gmx-xpm2ps.1 gromacs-2016.3/docs/man/gmx-xpm2ps.1
--- gromacs-2016.2/docs/man/gmx-xpm2ps.1	2017-02-07 10:53:50.000000000 +0000
+++ gromacs-2016.3/docs/man/gmx-xpm2ps.1	2017-03-13 17:31:00.000000000 +0000
@@ -1,6 +1,6 @@
 .\" Man page generated from reStructuredText.
 .
-.TH "GMX-XPM2PS" "1" "Feb 07, 2017" "2016.2" "GROMACS"
+.TH "GMX-XPM2PS" "1" "Mar 13, 2017" "2016.3" "GROMACS"
 .SH NAME
 gmx-xpm2ps \- Convert XPM (XPixelMap) matrices to postscript or XPM
 .
diff -Nru gromacs-2016.2/docs/user-guide/index.rst gromacs-2016.3/docs/user-guide/index.rst
--- gromacs-2016.2/docs/user-guide/index.rst	2016-07-09 00:55:38.000000000 +0000
+++ gromacs-2016.3/docs/user-guide/index.rst	2017-03-13 17:22:33.000000000 +0000
@@ -20,6 +20,7 @@
    :maxdepth: 2
 
    getting-started
+   system-preparation
    cutoff-schemes
    mdrun-features
    mdrun-performance
diff -Nru gromacs-2016.2/docs/user-guide/mdrun-performance.rst gromacs-2016.3/docs/user-guide/mdrun-performance.rst
--- gromacs-2016.2/docs/user-guide/mdrun-performance.rst	2016-10-28 18:24:31.000000000 +0000
+++ gromacs-2016.3/docs/user-guide/mdrun-performance.rst	2017-03-13 17:22:33.000000000 +0000
@@ -709,8 +709,12 @@
 -----------------------------------
 
 The current version works with GCN-based AMD GPUs, and NVIDIA CUDA
-GPUs. Make sure that you have the latest drivers installed. The
-minimum OpenCL version required is |REQUIRED_OPENCL_MIN_VERSION|. See
+GPUs. Make sure that you have the latest drivers installed. For AMD GPUs,
+Mesa version 17.0 or newer with LLVM 4.0 or newer is supported in addition
+to the proprietary driver. For NVIDIA GPUs, using the proprietary driver is
+required as the open source nouveau driver (available in Mesa) does not
+provide the OpenCL support.
+The minimum OpenCL version required is |REQUIRED_OPENCL_MIN_VERSION|. See
 also the :ref:`known limitations <opencl-known-limitations>`.
 
 Devices from the AMD GCN architectures (all series) and NVIDIA Fermi
diff -Nru gromacs-2016.2/docs/user-guide/system-preparation.rst gromacs-2016.3/docs/user-guide/system-preparation.rst
--- gromacs-2016.2/docs/user-guide/system-preparation.rst	1970-01-01 00:00:00.000000000 +0000
+++ gromacs-2016.3/docs/user-guide/system-preparation.rst	2017-03-13 17:22:33.000000000 +0000
@@ -0,0 +1,130 @@
+System preparation
+==================
+
+.. toctree::
+   :hidden:
+
+There are many ways to prepare a simulation system to run with
+|Gromacs|. These often vary with the kind of scientific question being
+considered, or the model physics involved. A protein-ligand atomistic
+free-energy simulation might need a multi-state topology, while a
+coarse-grained simulation might need to manage defaults that suit
+systems with higher density.
+
+Steps to consider
+-----------------
+
+The following general guidance should help with planning successful
+simulations. Some stages are optional for some kinds of simulations.
+
+1. Clearly identify the property or phenomena of interest to be
+   studied by performing the simulation. Do not continue further until
+   you are clear on this! Do not run your simulation and then seek to
+   work out how to use it to test your hypothesis, because it may be
+   unsuitable, or the required information was not saved.
+
+2. Select the appropriate tools to be able to perform the simulation
+   and observe the property or phenomena of interest. It is important
+   to read and familiarize yourself with publications by other
+   researchers on similar systems. Choices of tools include:
+
+   - software with which to perform the simulation (consideration of
+     force field may influence this decision)
+
+   - the force field, which describes how the particles within the
+     system interact with each other. Select one that is appropriate
+     for the system being studied and the property or phenomena of
+     interest. This is a very important and non-trivial step! Consider
+     now how you will analyze your simulation data to make your
+     observations.
+
+3. Obtain or generate the initial coordinate file for each molecule to
+   be placed within the system. Many different software packages are
+   able to build molecular structures and assemble them into suitable
+   configurations.
+
+4. Generate the raw starting structure for the system by placing the
+   molecules within the coordinate file as appropriate. Molecules may
+   be specifically placed or arranged randomly. Several non-|Gromacs|
+   tools are useful here; within |Gromacs| :ref:`gmx solvate`,
+   :ref:`gmx insert-molecules` and :ref:`gmx genconf` solve frequent
+   problems.
+
+5. Obtain or generate the topology file for the system, using (for
+   example) :ref:`gmx pdb2gmx`, :ref:`gmx x2top`, `SwissParam
+   <http://swissparam.ch/>`_ (for CHARMM forcefield), `PRODRG
+   <http://davapc1.bioch.dundee.ac.uk/cgi-bin/prodrg>`_ (for GROMOS96
+   43A1), `Automated Topology Builder
+   <http://compbio.biosci.uq.edu.au/atb/>`_ (for GROMOS96 53A6),
+   `MKTOP <http://www.aribeiro.net.br/mktop>`_ (for OPLS/AA) or your
+   favourite text editor in concert with chapter 5 of the |Gromacs|
+   `Reference Manual`_. For the AMBER force fields, `antechamber
+   <http://amber.scripps.edu/antechamber/antechamber.html>`_ or
+   `acpype <https://code.google.com/archive/p/acpype/>`_ might be
+   appropriate.
+
+6. Describe a simulation box (e.g. using :ref:`gmx editconf`) whose
+   size is appropriate for the eventual density you would like, fill
+   it with solvent (e.g. using :ref:`gmx solvate`), and add any
+   counter-ions needed to neutralize the system (e.g. using :ref:`gmx
+   grompp` and :ref:`gmx insert-molecules`). In these steps you may
+   need to edit your topology file to stay current with your
+   coordinate file.
+
+7. Run an energy minimization on the system (using :ref:`gmx grompp`
+   and :ref:`gmx mdrun`). This is required to sort out any bad
+   starting structures caused during generation of the system, which
+   may cause the production simulation to crash. It may be necessary
+   also to minimize your solute structure in vacuo before introducing
+   solvent molecules (or your lipid bilayer or whatever else). You
+   should consider using flexible water models and not using bond
+   constraints or frozen groups. The use of position restraints and/or
+   distance restraints should be evaluated carefully.
+
+8. Select the appropriate simulation parameters for the equilibration
+   simulation (defined in .mdp file). You need to choose simulation
+   parameters that are consistent with how force field was
+   derived. You may need to simulate at NVT with position restraints
+   on your solvent and/or solute to get the temperature almost right,
+   then relax to NPT to fix the density (which should be done with
+   Berendsen until after the density is stabilized, before a further
+   switch to a barostat that produces the correct ensemble), then move
+   further (if needed) to reach your production simulation ensemble
+   (e.g. NVT, NVE). If you have problems here with the system `blowing
+   up <http://www.gromacs.org/Documentation/Terminology/Blowing_Up>`_,
+   consider using the suggestions on that page, e.g. position
+   restraints on solutes, or not using bond constraints, or using
+   smaller integration timesteps, or several gentler heating stage(s).
+
+9. Run the equilibration simulation for sufficient time so that the
+   system relaxes sufficiently in the target ensemble to allow the
+   production run to be commenced (using :ref:`gmx grompp` and
+   :ref:`gmx mdrun`, then :ref:`gmx energy` and `trajectory
+   visualization tools
+   <http://www.gromacs.org/Documentation/How-tos/Trajectory_Visualization>`_).
+
+10. Select the appropriate simulation parameters for the production
+    simulation (defined in .mdp file). In particular, be careful not
+    to re-generate the velocities. You still need to be consistent
+    with how the force field was derived and how to measure the
+    property or phenomena of interest.
+
+.. _Reference Manual: `gmx-manual`_
+
+Tips and tricks
+---------------
+
+Database files
+^^^^^^^^^^^^^^
+
+The ``share/top`` directory of a |Gromacs| installation contains
+numerous plain-text helper files with the ``.dat`` file extension.
+Some of the command-line tools (see :doc:`cmdline`) refer to these,
+and each tool documents which files it uses, and how they are used.
+
+If you need to modify these files (e.g. to introduce new atom types
+with VDW radii into ``vdwradii.dat``), you can copy the file from your
+installation directory into your working directory, and the |Gromacs|
+tools will automatically load the copy from your working directory
+rather than the standard one. To suppress all the standard
+definitions, use an empty file in the working directory.
diff -Nru gromacs-2016.2/INSTALL gromacs-2016.3/INSTALL
--- gromacs-2016.2/INSTALL	2017-02-07 10:53:54.000000000 +0000
+++ gromacs-2016.3/INSTALL	2017-03-13 17:31:06.000000000 +0000
@@ -6,7 +6,7 @@
 Introduction to building GROMACS
 ================================
 
-These instructions pertain to building GROMACS 2016.2. You might also
+These instructions pertain to building GROMACS 2016.3. You might also
 want to check the up-to-date installation instructions.
 
 
@@ -29,8 +29,8 @@
 
 Or, as a sequence of commands to execute:
 
-   tar xfz gromacs-2016.2.tar.gz
-   cd gromacs-2016.2
+   tar xfz gromacs-2016.3.tar.gz
+   cd gromacs-2016.3
    mkdir build
    cd build
    cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
@@ -134,11 +134,19 @@
 frequently provides the best performance.
 
 You should strive to use the most recent version of your compiler.
-Minimum supported compiler versions are * GNU (gcc) 4.6 * Intel (icc)
-14 * LLVM (clang) 3.4 * Microsoft (MSVC) 2015 Other compilers may work
-(Cray, Pathscale, older clang) but do not offer competitive
-performance. We recommend against PGI because the performance with C++
-is very bad.
+Minimum supported compiler versions are
+
+* GNU (gcc) 4.6
+
+* Intel (icc) 14
+
+* LLVM (clang) 3.4
+
+* Microsoft (MSVC) 2015
+
+Other compilers may work (Cray, Pathscale, older clang) but do not
+offer competitive performance. We recommend against PGI because the
+performance with C++ is very bad.
 
 You may also need the most recent version of other compiler toolchain
 components beside the compiler itself (e.g. assembler or linker);
@@ -395,8 +403,8 @@
 code you want to build. For example, download the source tarball and
 use
 
-   tar xfz gromacs-2016.2.tgz
-   cd gromacs-2016.2
+   tar xfz gromacs-2016.3.tgz
+   cd gromacs-2016.3
    mkdir build-gromacs
    cd build-gromacs
    cmake ..
@@ -930,7 +938,7 @@
 "-DREGRESSIONTEST_DOWNLOAD", and run "make check". GROMACS will
 automatically download and run the tests for you. Alternatively, you
 can download and unpack the GROMACS regression test suite
-http://gerrit.gromacs.org/download/regressiontests-2016.2.tar.gz
+http://gerrit.gromacs.org/download/regressiontests-2016.3.tar.gz
 tarball yourself and use the advanced "cmake" option
 "REGRESSIONTEST_PATH" to specify the path to the unpacked tarball,
 which will then be used for testing. If the above does not work, then
diff -Nru gromacs-2016.2/src/contrib/fftw/CMakeLists.txt gromacs-2016.3/src/contrib/fftw/CMakeLists.txt
--- gromacs-2016.2/src/contrib/fftw/CMakeLists.txt	2016-10-25 09:50:19.000000000 +0000
+++ gromacs-2016.3/src/contrib/fftw/CMakeLists.txt	2017-03-13 17:22:33.000000000 +0000
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -73,7 +73,12 @@
     # Support for --enable-avx2 was only added in 3.3.5, but
     # configuring with it is at worst a warning, even on an earlier
     # version.
+if((CMAKE_COMPILER_IS_GNUCC AND (C_COMPILER_VERSION VERSION_GREATER 4.9 OR CXX_COMPILER_VERSION VERSION_GREATER 4.9)) OR
+   (CMAKE_C_COMPILER_ID MATCHES "Clang" AND (C_COMPILER_VERSION VERSION_GREATER 3.9 OR CXX_COMPILER_VERSION VERSION_GREATER 3.9)))
     set(_fftw_simd_support_level --enable-sse2;--enable-avx;--enable-avx2;--enable-avx512)
+elseif()
+    set(_fftw_simd_support_level --enable-sse2;--enable-avx;--enable-avx2)
+endif()
 elseif(${GMX_SIMD} MATCHES "^(VSX)")
     set(_fftw_simd_support_level --enable-vsx)
 endif()
diff -Nru gromacs-2016.2/src/gromacs/gmxana/gmx_do_dssp.cpp gromacs-2016.3/src/gromacs/gmxana/gmx_do_dssp.cpp
--- gromacs-2016.2/src/gromacs/gmxana/gmx_do_dssp.cpp	2016-07-09 00:55:38.000000000 +0000
+++ gromacs-2016.3/src/gromacs/gmxana/gmx_do_dssp.cpp	2017-03-13 17:22:33.000000000 +0000
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -423,8 +423,8 @@
     }
     fprintf(fp, "\n");
 
-    /* now print percentages */
-    fprintf(fp, "%-8s %5.2f", "# SS %", total_count / static_cast<real>(mat->nx * mat->ny));
+    /* now print probabilities */
+    fprintf(fp, "%-8s %5.2f", "# SS pr.", total_count / static_cast<real>(mat->nx * mat->ny));
     for (s = 0; s < static_cast<size_t>(mat->nmap); s++)
     {
         fprintf(fp, " %5.2f", total[s] / static_cast<real>(mat->nx * mat->ny));
diff -Nru gromacs-2016.2/src/gromacs/gmxana/gmx_mindist.cpp gromacs-2016.3/src/gromacs/gmxana/gmx_mindist.cpp
--- gromacs-2016.2/src/gromacs/gmxana/gmx_mindist.cpp	2016-12-06 18:53:27.000000000 +0000
+++ gromacs-2016.3/src/gromacs/gmxana/gmx_mindist.cpp	2017-03-13 17:22:33.000000000 +0000
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -413,15 +413,16 @@
         sprintf(buf, "%simum Distance", bMin ? "Min" : "Max");
         respertime = xvgropen(rfile, buf, output_env_get_time_label(oenv), "Distance (nm)", oenv);
         xvgr_legend(respertime, ng-1, (const char**)leg, oenv);
-        if (bPrintResName)
+        if (bPrintResName && output_env_get_print_xvgr_codes(oenv) )
         {
             fprintf(respertime, "# ");
+
+            for (j = 0; j < nres; j++)
+            {
+                fprintf(respertime, "%s%d ", *(atoms->resinfo[atoms->atom[index[0][residue[j]]].resind].name), atoms->atom[index[0][residue[j]]].resind);
+            }
+            fprintf(respertime, "\n");
         }
-        for (j = 0; j < nres; j++)
-        {
-            fprintf(respertime, "%s%d ", *(atoms->resinfo[atoms->atom[index[0][residue[j]]].resind].name), atoms->atom[index[0][residue[j]]].resind);
-        }
-        fprintf(respertime, "\n");
 
     }
 
diff -Nru gromacs-2016.2/src/gromacs/gmxana/gmx_traj.cpp gromacs-2016.3/src/gromacs/gmxana/gmx_traj.cpp
--- gromacs-2016.2/src/gromacs/gmxana/gmx_traj.cpp	2016-12-06 18:53:27.000000000 +0000
+++ gromacs-2016.3/src/gromacs/gmxana/gmx_traj.cpp	2017-03-13 17:22:33.000000000 +0000
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -461,7 +461,7 @@
             svmul(scale, sum[index[i]], sum[index[i]]);
         }
 
-        fp = xvgropen(xname, title, "Atom", "", oenv);
+        fp = xvgropen(xname, title, "Atom", "Spatial component", oenv);
         for (i = 0; i < isize; i++)
         {
             fprintf(fp, "%-5d  %10.3f  %10.3f  %10.3f\n", 1+i,
diff -Nru gromacs-2016.2/src/gromacs/gmxana/gmx_trjconv.cpp gromacs-2016.3/src/gromacs/gmxana/gmx_trjconv.cpp
--- gromacs-2016.2/src/gromacs/gmxana/gmx_trjconv.cpp	2016-12-06 18:53:27.000000000 +0000
+++ gromacs-2016.3/src/gromacs/gmxana/gmx_trjconv.cpp	2017-03-13 17:22:33.000000000 +0000
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -665,10 +665,6 @@
         "   results if you in fact have a cluster. Luckily that can be checked",
         "   afterwards using a trajectory viewer. Note also that if your molecules",
         "   are broken this will not work either.",
-        "",
-        "   The separate option [TT]-clustercenter[tt] can be used to specify an",
-        "   approximate center for the cluster. This is useful e.g. if you have",
-        "   two big vesicles, and you want to maintain their relative positions.",
         " * [TT]whole[tt] only makes broken molecules whole.",
         "",
 
diff -Nru gromacs-2016.2/src/gromacs/gmxana/gmx_tune_pme.cpp gromacs-2016.3/src/gromacs/gmxana/gmx_tune_pme.cpp
--- gromacs-2016.2/src/gromacs/gmxana/gmx_tune_pme.cpp	2017-02-05 20:30:25.000000000 +0000
+++ gromacs-2016.3/src/gromacs/gmxana/gmx_tune_pme.cpp	2017-03-13 17:22:33.000000000 +0000
@@ -659,17 +659,17 @@
      * gmx_print_version_info() in the GMX_MPI section */
     const char match_mpi[]     = "MPI library:        MPI";
     const char match_mdrun[]   = "Executable: ";
-    const char match_gpu[]     = "GPU support:        enabled";
+    const char match_nogpu[]   = "GPU support:        disabled";
     gmx_bool   bMdrun          = FALSE;
     gmx_bool   bMPI            = FALSE;
-    gmx_bool   bHaveGpuSupport = FALSE;
+    gmx_bool   bHaveGpuSupport = TRUE;
 
     /* Run a small test to see whether mpirun + mdrun work  */
     fprintf(stdout, "Making sure that mdrun can be executed. ");
     if (bThreads)
     {
         snew(command, std::strlen(cmd_mdrun) + std::strlen(cmd_np) + std::strlen(filename) + 50);
-        sprintf(command, "%s%s-version -maxh 0.001 1> %s 2>&1", cmd_mdrun, cmd_np, filename);
+        sprintf(command, "%s%s -version -maxh 0.001 1> %s 2>&1", cmd_mdrun, cmd_np, filename);
     }
     else
     {
@@ -702,9 +702,9 @@
             {
                 bMPI = TRUE;
             }
-            if (str_starts(line, match_gpu) )
+            if (str_starts(line, match_nogpu) )
             {
-                bHaveGpuSupport = TRUE;
+                bHaveGpuSupport = FALSE;
             }
         }
     }
diff -Nru gromacs-2016.2/src/gromacs/gmxpreprocess/insert-molecules.cpp gromacs-2016.3/src/gromacs/gmxpreprocess/insert-molecules.cpp
--- gromacs-2016.2/src/gromacs/gmxpreprocess/insert-molecules.cpp	2016-12-06 18:53:27.000000000 +0000
+++ gromacs-2016.3/src/gromacs/gmxpreprocess/insert-molecules.cpp	2017-03-13 17:22:33.000000000 +0000
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -409,8 +409,10 @@
         "inserted molecule is less than the sum based on the van der Waals",
         "radii of both atoms. A database ([TT]vdwradii.dat[tt]) of van der",
         "Waals radii is read by the program, and the resulting radii scaled",
-        "by [TT]-scale[tt]. If radii are not found in the database, those"
+        "by [TT]-scale[tt]. If radii are not found in the database, those",
         "atoms are assigned the (pre-scaled) distance [TT]-radius[tt].",
+        "Note that the usefulness of those radii depends on the atom names,",
+        "and thus varies widely with force field.",
         "",
         "A total of [TT]-nmol[tt] * [TT]-try[tt] insertion attempts are made",
         "before giving up. Increase [TT]-try[tt] if you have several small",
diff -Nru gromacs-2016.2/src/gromacs/gmxpreprocess/readir.cpp gromacs-2016.3/src/gromacs/gmxpreprocess/readir.cpp
--- gromacs-2016.2/src/gromacs/gmxpreprocess/readir.cpp	2016-12-06 18:53:27.000000000 +0000
+++ gromacs-2016.3/src/gromacs/gmxpreprocess/readir.cpp	2017-03-13 17:22:33.000000000 +0000
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -811,7 +811,7 @@
         if (expand->nstTij > 0)
         {
             sprintf(err_buf, "nstlog must be non-zero");
-            CHECK(ir->nstlog != 0);
+            CHECK(ir->nstlog == 0);
             sprintf(err_buf, "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
                     expand->nstTij, ir->nstlog);
             CHECK((expand->nstTij % ir->nstlog) != 0);
diff -Nru gromacs-2016.2/src/gromacs/gmxpreprocess/solvate.cpp gromacs-2016.3/src/gromacs/gmxpreprocess/solvate.cpp
--- gromacs-2016.2/src/gromacs/gmxpreprocess/solvate.cpp	2016-07-09 00:55:39.000000000 +0000
+++ gromacs-2016.3/src/gromacs/gmxpreprocess/solvate.cpp	2017-03-13 17:22:33.000000000 +0000
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -491,50 +491,86 @@
 }
 
 /*! \brief
- * Removes solvent molecules that overlap with the solute, and optionally also
- * those that are outside a given shell radius from the solute.
+ * Remove all solvent molecules outside a give radius from the solute.
  *
- * \param[in,out] atoms      Solvent atoms.
- * \param[in,out] x          Solvent positions.
- * \param[in,out] v          Solvent velocities (can be empty).
- * \param[in,out] r          Solvent exclusion radii.
- * \param[in]     pbc        PBC information.
- * \param[in]     x_solute   Solute positions.
- * \param[in]     r_solute   Solute exclusion radii.
- * \param[in]     rshell     If >0, only keep solvent atoms within a shell of
- *     this size from the solute.
+ * \param[in,out] atoms     Solvent atoms.
+ * \param[in,out] x_solvent Solvent positions.
+ * \param[in,out] v_solvent Solvent velocities.
+ * \param[in,out] r         Atomic exclusion radii.
+ * \param[in]     pbc       PBC information.
+ * \param[in]     x_solute  Solute positions.
+ * \param[in]     rshell    The radius outside the solute molecule.
  */
-static void removeSoluteOverlap(t_atoms *atoms, std::vector<RVec> *x,
-                                std::vector<RVec> *v, std::vector<real> *r,
-                                const t_pbc &pbc,
-                                const std::vector<RVec> &x_solute,
-                                const std::vector<real> &r_solute,
-                                real rshell)
+static void removeSolventOutsideShell(t_atoms                 *atoms,
+                                      std::vector<RVec>       *x_solvent,
+                                      std::vector<RVec>       *v_solvent,
+                                      std::vector<real>       *r,
+                                      const t_pbc             &pbc,
+                                      const std::vector<RVec> &x_solute,
+                                      real                     rshell)
 {
-    const real                          maxRadius1
-        = *std::max_element(r->begin(), r->end());
-    const real                          maxRadius2
-        = *std::max_element(r_solute.begin(), r_solute.end());
-
     gmx::AtomsRemover                   remover(*atoms);
-    // If rshell is >0, the neighborhood search looks at all pairs
-    // within rshell, and unmarks those that are within the cutoff.
-    // This line marks everything, so that solvent outside rshell remains
-    // marked after the loop.
-    // Without rshell, the neighborhood search only marks the overlapping
-    // solvent atoms, and all others are left alone.
-    if (rshell > 0.0)
+    gmx::AnalysisNeighborhood           nb;
+    nb.setCutoff(rshell);
+    gmx::AnalysisNeighborhoodPositions  posSolute(x_solute);
+    gmx::AnalysisNeighborhoodSearch     search     = nb.initSearch(&pbc, posSolute);
+    gmx::AnalysisNeighborhoodPositions  pos(*x_solvent);
+    gmx::AnalysisNeighborhoodPairSearch pairSearch = search.startPairSearch(pos);
+    gmx::AnalysisNeighborhoodPair       pair;
+
+    // Remove everything
+    remover.markAll();
+    // Now put back those within the shell without checking for overlap
+    while (pairSearch.findNextPair(&pair))
+    {
+        remover.markResidue(*atoms, pair.testIndex(), false);
+        pairSearch.skipRemainingPairsForTestPosition();
+    }
+    remover.removeMarkedElements(x_solvent);
+    if (!v_solvent->empty())
     {
-        remover.markAll();
+        remover.removeMarkedElements(v_solvent);
     }
+    remover.removeMarkedElements(r);
+    const int originalAtomCount = atoms->nr;
+    remover.removeMarkedAtoms(atoms);
+    fprintf(stderr, "Removed %d solvent atoms more than %f nm from solute.\n",
+            originalAtomCount - atoms->nr, rshell);
+}
 
+/*! \brief
+ * Removes solvent molecules that overlap with the solute.
+ *
+ * \param[in,out] atoms    Solvent atoms.
+ * \param[in,out] x        Solvent positions.
+ * \param[in,out] v        Solvent velocities (can be empty).
+ * \param[in,out] r        Solvent exclusion radii.
+ * \param[in]     pbc      PBC information.
+ * \param[in]     x_solute Solute positions.
+ * \param[in]     r_solute Solute exclusion radii.
+ */
+static void removeSolventOverlappingWithSolute(t_atoms                 *atoms,
+                                               std::vector<RVec>       *x,
+                                               std::vector<RVec>       *v,
+                                               std::vector<real>       *r,
+                                               const t_pbc             &pbc,
+                                               const std::vector<RVec> &x_solute,
+                                               const std::vector<real> &r_solute)
+{
+    gmx::AtomsRemover             remover(*atoms);
+    const real                    maxRadius1
+        = *std::max_element(r->begin(), r->end());
+    const real                    maxRadius2
+        = *std::max_element(r_solute.begin(), r_solute.end());
+
+    // Now check for overlap.
     gmx::AnalysisNeighborhood           nb;
-    nb.setCutoff(std::max(maxRadius1 + maxRadius2, rshell));
+    gmx::AnalysisNeighborhoodPair       pair;
+    nb.setCutoff(maxRadius1 + maxRadius2);
     gmx::AnalysisNeighborhoodPositions  posSolute(x_solute);
     gmx::AnalysisNeighborhoodSearch     search     = nb.initSearch(&pbc, posSolute);
     gmx::AnalysisNeighborhoodPositions  pos(*x);
     gmx::AnalysisNeighborhoodPairSearch pairSearch = search.startPairSearch(pos);
-    gmx::AnalysisNeighborhoodPair       pair;
     while (pairSearch.findNextPair(&pair))
     {
         if (remover.isMarked(pair.testIndex()))
@@ -647,8 +683,14 @@
     }
     if (top->atoms.nr > 0)
     {
-        removeSoluteOverlap(atoms_solvt, &x_solvt, &v_solvt, &exclusionDistances_solvt, pbc,
-                            *x, exclusionDistances, rshell);
+        if (rshell > 0.0)
+        {
+            removeSolventOutsideShell(atoms_solvt, &x_solvt,  &v_solvt,
+                                      &exclusionDistances_solvt, pbc, *x, rshell);
+        }
+        removeSolventOverlappingWithSolute(atoms_solvt, &x_solvt, &v_solvt,
+                                           &exclusionDistances_solvt, pbc, *x,
+                                           exclusionDistances);
     }
 
     if (max_sol > 0 && atoms_solvt->nres > max_sol)
@@ -827,9 +869,11 @@
         "the solvent molecule is less than the sum of the scaled van der Waals",
         "radii of both atoms. A database ([TT]vdwradii.dat[tt]) of van der",
         "Waals radii is read by the program, and the resulting radii scaled",
-        "by [TT]-scale[tt]. If radii are not found in the database, those"
-        "atoms are assigned the (pre-scaled) distance [TT]-radius[tt].[PAR]",
-
+        "by [TT]-scale[tt]. If radii are not found in the database, those",
+        "atoms are assigned the (pre-scaled) distance [TT]-radius[tt].",
+        "Note that the usefulness of those radii depends on the atom names,",
+        "and thus varies widely with force field.",
+        "",
         "The default solvent is Simple Point Charge water (SPC), with coordinates ",
         "from [TT]$GMXLIB/spc216.gro[tt]. These coordinates can also be used",
         "for other 3-site water models, since a short equibilibration will remove",
diff -Nru gromacs-2016.2/src/gromacs/gmxpreprocess/tests/refdata/SolvateTest_cs_box_Works.xml gromacs-2016.3/src/gromacs/gmxpreprocess/tests/refdata/SolvateTest_cs_box_Works.xml
--- gromacs-2016.2/src/gromacs/gmxpreprocess/tests/refdata/SolvateTest_cs_box_Works.xml	1970-01-01 00:00:00.000000000 +0000
+++ gromacs-2016.3/src/gromacs/gmxpreprocess/tests/refdata/SolvateTest_cs_box_Works.xml	2017-03-13 17:22:33.000000000 +0000
@@ -0,0 +1,12 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+  <OutputFiles Name="Files">
+    <File Name="-o">
+      <GroFile Name="Header">
+        <String Name="Title">Generated by gmx solvate</String>
+        <Int Name="Number of atoms">141</Int>
+      </GroFile>
+    </File>
+  </OutputFiles>
+</ReferenceData>
diff -Nru gromacs-2016.2/src/gromacs/gmxpreprocess/tests/refdata/SolvateTest_cs_cp_p_Works.xml gromacs-2016.3/src/gromacs/gmxpreprocess/tests/refdata/SolvateTest_cs_cp_p_Works.xml
--- gromacs-2016.2/src/gromacs/gmxpreprocess/tests/refdata/SolvateTest_cs_cp_p_Works.xml	1970-01-01 00:00:00.000000000 +0000
+++ gromacs-2016.3/src/gromacs/gmxpreprocess/tests/refdata/SolvateTest_cs_cp_p_Works.xml	2017-03-13 17:22:33.000000000 +0000
@@ -0,0 +1,12 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+  <OutputFiles Name="Files">
+    <File Name="-o">
+      <GroFile Name="Header">
+        <String Name="Title">Test system for solvate/insert-molecules</String>
+        <Int Name="Number of atoms">2664</Int>
+      </GroFile>
+    </File>
+  </OutputFiles>
+</ReferenceData>
diff -Nru gromacs-2016.2/src/gromacs/gmxpreprocess/tests/refdata/SolvateTest_cs_cp_Works.xml gromacs-2016.3/src/gromacs/gmxpreprocess/tests/refdata/SolvateTest_cs_cp_Works.xml
--- gromacs-2016.2/src/gromacs/gmxpreprocess/tests/refdata/SolvateTest_cs_cp_Works.xml	1970-01-01 00:00:00.000000000 +0000
+++ gromacs-2016.3/src/gromacs/gmxpreprocess/tests/refdata/SolvateTest_cs_cp_Works.xml	2017-03-13 17:22:33.000000000 +0000
@@ -0,0 +1,12 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+  <OutputFiles Name="Files">
+    <File Name="-o">
+      <GroFile Name="Header">
+        <String Name="Title">Test system for solvate/insert-molecules</String>
+        <Int Name="Number of atoms">2664</Int>
+      </GroFile>
+    </File>
+  </OutputFiles>
+</ReferenceData>
diff -Nru gromacs-2016.2/src/gromacs/gmxpreprocess/tests/refdata/SolvateTest_shell_Works.xml gromacs-2016.3/src/gromacs/gmxpreprocess/tests/refdata/SolvateTest_shell_Works.xml
--- gromacs-2016.2/src/gromacs/gmxpreprocess/tests/refdata/SolvateTest_shell_Works.xml	1970-01-01 00:00:00.000000000 +0000
+++ gromacs-2016.3/src/gromacs/gmxpreprocess/tests/refdata/SolvateTest_shell_Works.xml	2017-03-13 17:22:33.000000000 +0000
@@ -0,0 +1,12 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+  <OutputFiles Name="Files">
+    <File Name="-o">
+      <GroFile Name="Header">
+        <String Name="Title">Test system for solvate/insert-molecules</String>
+        <Int Name="Number of atoms">762</Int>
+      </GroFile>
+    </File>
+  </OutputFiles>
+</ReferenceData>
diff -Nru gromacs-2016.2/src/gromacs/gmxpreprocess/tests/solvate.cpp gromacs-2016.3/src/gromacs/gmxpreprocess/tests/solvate.cpp
--- gromacs-2016.2/src/gromacs/gmxpreprocess/tests/solvate.cpp	2016-07-09 00:55:39.000000000 +0000
+++ gromacs-2016.3/src/gromacs/gmxpreprocess/tests/solvate.cpp	2017-03-13 17:22:33.000000000 +0000
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -45,8 +45,11 @@
 #include "gromacs/gmxpreprocess/solvate.h"
 
 #include "gromacs/utility/futil.h"
+#include "gromacs/utility/textreader.h"
 
 #include "testutils/cmdlinetest.h"
+#include "testutils/conftest.h"
+#include "testutils/refdata.h"
 #include "testutils/testfilemanager.h"
 #include "testutils/textblockmatchers.h"
 
@@ -54,14 +57,14 @@
 {
 
 using gmx::test::CommandLine;
-using gmx::test::NoTextMatch;
+using gmx::test::ConfMatch;
 
 class SolvateTest : public gmx::test::CommandLineTestBase
 {
     public:
         SolvateTest()
         {
-            setOutputFile("-o", "out.gro", NoTextMatch());
+            setOutputFile("-o", "out.gro", ConfMatch());
         }
 
         void runTest(const CommandLine &args)
@@ -70,6 +73,7 @@
             cmdline.merge(args);
 
             ASSERT_EQ(0, gmx_solvate(cmdline.argc(), cmdline.argv()));
+            checkOutputFiles();
         }
 };
 
@@ -108,5 +112,17 @@
 
     runTest(CommandLine(cmdline));
 }
+
+TEST_F(SolvateTest, shell_Works)
+{
+    // use default solvent box (-cs without argument)
+    const char *const cmdline[] = {
+        "solvate", "-cs"
+    };
+    setInputFile("-cp", "spc-and-methanol.gro");
+    commandLine().addOption("-shell", 1.0);
+
+    runTest(CommandLine(cmdline));
+}
 
 } // namespace
diff -Nru gromacs-2016.2/src/gromacs/listed-forces/pairs.cpp gromacs-2016.3/src/gromacs/listed-forces/pairs.cpp
--- gromacs-2016.2/src/gromacs/listed-forces/pairs.cpp	2016-07-09 00:55:39.000000000 +0000
+++ gromacs-2016.3/src/gromacs/listed-forces/pairs.cpp	2017-03-13 17:22:33.000000000 +0000
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -607,7 +607,7 @@
         pbc_dx_aiuc(pbc, xi, xj, dr);
 
         T rsq   = dr[XX]*dr[XX] + dr[YY]*dr[YY] + dr[ZZ]*dr[ZZ];
-        T rinv  = invsqrt(rsq);
+        T rinv  = gmx::invsqrt(rsq);
         T rinv2 = rinv*rinv;
         T rinv6 = rinv2*rinv2*rinv2;
 
diff -Nru gromacs-2016.2/src/gromacs/mdlib/sim_util.cpp gromacs-2016.3/src/gromacs/mdlib/sim_util.cpp
--- gromacs-2016.2/src/gromacs/mdlib/sim_util.cpp	2017-02-05 20:30:25.000000000 +0000
+++ gromacs-2016.3/src/gromacs/mdlib/sim_util.cpp	2017-03-13 17:22:33.000000000 +0000
@@ -2574,12 +2574,22 @@
             elapsed_time_over_all_ranks,
             elapsed_time_over_all_threads,
             elapsed_time_over_all_threads_over_all_ranks;
+    /* Control whether it is valid to print a report. Only the
+       simulation master may print, but it should not do so if the run
+       terminated e.g. before a scheduled reset step. This is
+       complicated by the fact that PME ranks are unaware of the
+       reason why they were sent a pmerecvqxFINISH. To avoid
+       communication deadlocks, we always do the communication for the
+       report, even if we've decided not to write the report, because
+       how long it takes to finish the run is not important when we've
+       decided not to report on the simulation performance. */
+    bool    printReport = SIMMASTER(cr);
 
     if (!walltime_accounting_get_valid_finish(walltime_accounting))
     {
         md_print_warn(cr, fplog,
                       "Simulation ended prematurely, no performance report will be written.");
-        return;
+        printReport = false;
     }
 
     if (cr->nnodes > 1)
@@ -2617,7 +2627,7 @@
     }
 #endif
 
-    if (SIMMASTER(cr))
+    if (printReport)
     {
         print_flop(fplog, nrnb_tot, &nbfs, &mflop);
     }
@@ -2640,7 +2650,7 @@
     wallcycle_scale_by_num_threads(wcycle, cr->duty == DUTY_PME, nthreads_pp, nthreads_pme);
     auto cycle_sum(wallcycle_sum(cr, wcycle));
 
-    if (SIMMASTER(cr))
+    if (printReport)
     {
         struct gmx_wallclock_gpu_t* gputimes = use_GPU(nbv) ? nbnxn_gpu_get_timings(nbv->gpu_nbv) : NULL;
 
diff -Nru gromacs-2016.2/src/gromacs/simd/impl_ibm_vsx/impl_ibm_vsx_general.h gromacs-2016.3/src/gromacs/simd/impl_ibm_vsx/impl_ibm_vsx_general.h
--- gromacs-2016.2/src/gromacs/simd/impl_ibm_vsx/impl_ibm_vsx_general.h	2016-07-09 00:55:39.000000000 +0000
+++ gromacs-2016.3/src/gromacs/simd/impl_ibm_vsx/impl_ibm_vsx_general.h	2017-03-13 17:22:33.000000000 +0000
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -43,7 +43,7 @@
 simdPrefetch(const void * m)
 {
 #if defined(__ibmxl__) || defined(__xlC__)
-    __dcbt(m);
+    __dcbt((void *)m);
 #elif defined __GNUC__
     __builtin_prefetch(m);
 #endif
diff -Nru gromacs-2016.2/src/gromacs/simd/impl_ibm_vsx/impl_ibm_vsx_simd4_float.h gromacs-2016.3/src/gromacs/simd/impl_ibm_vsx/impl_ibm_vsx_simd4_float.h
--- gromacs-2016.2/src/gromacs/simd/impl_ibm_vsx/impl_ibm_vsx_simd4_float.h	2016-07-09 00:55:39.000000000 +0000
+++ gromacs-2016.3/src/gromacs/simd/impl_ibm_vsx/impl_ibm_vsx_simd4_float.h	2017-03-13 17:22:33.000000000 +0000
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -105,25 +105,15 @@
 static inline Simd4Float gmx_simdcall
 load4U(const float *m)
 {
-#if defined(__ibmxl__) || defined(__xlC__)
-    return {
-               vec_xlw4(0, const_cast<float *>(m))
-    }
-#else
     return {
                *reinterpret_cast<const __vector float *>(m)
     };
-#endif
 }
 
 static inline void gmx_simdcall
 store4U(float *m, Simd4Float a)
 {
-#if defined(__ibmxl__) || defined(__xlC__)
-    vec_xstw4(a.simdInternal_, 0, m);
-#else
     *reinterpret_cast<__vector float *>(m) = a.simdInternal_;
-#endif
 }
 
 static inline Simd4Float gmx_simdcall
diff -Nru gromacs-2016.2/src/gromacs/simd/impl_ibm_vsx/impl_ibm_vsx_simd_double.h gromacs-2016.3/src/gromacs/simd/impl_ibm_vsx/impl_ibm_vsx_simd_double.h
--- gromacs-2016.2/src/gromacs/simd/impl_ibm_vsx/impl_ibm_vsx_simd_double.h	2016-07-09 00:55:39.000000000 +0000
+++ gromacs-2016.3/src/gromacs/simd/impl_ibm_vsx/impl_ibm_vsx_simd_double.h	2017-03-13 17:22:33.000000000 +0000
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -99,19 +99,8 @@
         __vector vsxBool int  simdInternal_;
 };
 
-// The VSX load & store operations are a bit of a mess. The interface is different
-// for xlc version 12, xlc version 13, and gcc. Long-term IBM recommends
-// simply using pointer dereferencing both for aligned and unaligned loads.
-// That's nice, but unfortunately xlc still bugs out when the pointer is
-// not aligned. Sticking to vec_xl/vec_xst isn't a solution either, since
-// that appears to be buggy for some _aligned_ loads :-)
-//
-// For now, we use pointer dereferencing for all aligned load/stores, and
-// for unaligned ones with gcc. On xlc we use vec_xlw4/vec_xstw4 for
-// unaligned memory operations. The latest docs recommend using the overloaded
-// vec_xl/vec_xst, but that is not supported on xlc version 12. We'll
-// revisit things once xlc is a bit more stable - for now you probably want
-// to stick to gcc...
+// Note that the interfaces we use here have been a mess in xlc;
+// currently version 13.1.5 is required.
 
 static inline SimdDouble gmx_simdcall
 simdLoad(const double *m)
@@ -130,25 +119,15 @@
 static inline SimdDouble gmx_simdcall
 simdLoadU(const double *m)
 {
-#if defined(__ibmxl__) || defined(__xlC__)
-    return {
-               vec_xlw4(0, const_cast<double *>(m))
-    }
-#else
     return {
                *reinterpret_cast<const __vector double *>(m)
     };
-#endif
 }
 
 static inline void gmx_simdcall
 storeU(double *m, SimdDouble a)
 {
-#if defined(__ibmxl__) || defined(__xlC__)
-    vec_xstw4(a.simdInternal_, 0, m);
-#else
     *reinterpret_cast<__vector double *>(m) = a.simdInternal_;
-#endif
 }
 
 static inline SimdDouble gmx_simdcall
diff -Nru gromacs-2016.2/src/gromacs/simd/impl_ibm_vsx/impl_ibm_vsx_simd_float.h gromacs-2016.3/src/gromacs/simd/impl_ibm_vsx/impl_ibm_vsx_simd_float.h
--- gromacs-2016.2/src/gromacs/simd/impl_ibm_vsx/impl_ibm_vsx_simd_float.h	2016-07-09 00:55:39.000000000 +0000
+++ gromacs-2016.3/src/gromacs/simd/impl_ibm_vsx/impl_ibm_vsx_simd_float.h	2017-03-13 17:22:33.000000000 +0000
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -99,19 +99,8 @@
         __vector vsxBool int  simdInternal_;
 };
 
-// The VSX load & store operations are a bit of a mess. The interface is different
-// for xlc version 12, xlc version 13, and gcc. Long-term IBM recommends
-// simply using pointer dereferencing both for aligned and unaligned loads.
-// That's nice, but unfortunately xlc still bugs out when the pointer is
-// not aligned. Sticking to vec_xl/vec_xst isn't a solution either, since
-// that appears to be buggy for some _aligned_ loads :-)
-//
-// For now, we use pointer dereferencing for all aligned load/stores, and
-// for unaligned ones with gcc. On xlc we use vec_xlw4/vec_xstw4 for
-// unaligned memory operations. The latest docs recommend using the overloaded
-// vec_xl/vec_xst, but that is not supported on xlc version 12. We'll
-// revisit things once xlc is a bit more stable - for now you probably want
-// to stick to gcc...
+// Note that the interfaces we use here have been a mess in xlc;
+// currently version 13.1.5 is required.
 
 static inline SimdFloat gmx_simdcall
 simdLoad(const float *m)
@@ -130,25 +119,15 @@
 static inline SimdFloat gmx_simdcall
 simdLoadU(const float *m)
 {
-#if defined(__ibmxl__) || defined(__xlC__)
-    return {
-               vec_xlw4(0, const_cast<float *>(m))
-    }
-#else
     return {
                *reinterpret_cast<const __vector float *>(m)
     };
-#endif
 }
 
 static inline void gmx_simdcall
 storeU(float *m, SimdFloat a)
 {
-#if defined(__ibmxl__) || defined(__xlC__)
-    vec_xstw4(a.simdInternal_, 0, m);
-#else
     *reinterpret_cast<__vector float *>(m) = a.simdInternal_;
-#endif
 }
 
 static inline SimdFloat gmx_simdcall
@@ -176,25 +155,15 @@
 static inline SimdFInt32 gmx_simdcall
 simdLoadUFI(const std::int32_t *m)
 {
-#if defined(__ibmxl__) || defined(__xlC__)
-    return {
-               vec_xlw4(0, const_cast<int *>(m))
-    }
-#else
     return {
                *reinterpret_cast<const __vector int *>(m)
     };
-#endif
 }
 
 static inline void gmx_simdcall
 storeU(std::int32_t * m, SimdFInt32 a)
 {
-#if defined(__ibmxl__) || defined(__xlC__)
-    vec_xstw4(a.simdInternal_, 0, m);
-#else
     *reinterpret_cast<__vector int *>(m) = a.simdInternal_;
-#endif
 }
 
 static inline SimdFInt32 gmx_simdcall
diff -Nru gromacs-2016.2/src/gromacs/simd/impl_ibm_vsx/impl_ibm_vsx_util_float.h gromacs-2016.3/src/gromacs/simd/impl_ibm_vsx/impl_ibm_vsx_util_float.h
--- gromacs-2016.2/src/gromacs/simd/impl_ibm_vsx/impl_ibm_vsx_util_float.h	2016-07-09 00:55:39.000000000 +0000
+++ gromacs-2016.3/src/gromacs/simd/impl_ibm_vsx/impl_ibm_vsx_util_float.h	2017-03-13 17:22:33.000000000 +0000
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -55,15 +55,17 @@
                     SimdFloat *          v2,
                     SimdFloat *          v3)
 {
-    *v0 = simdLoad( base + align * offset[0] );
-    *v1 = simdLoad( base + align * offset[1] );
-    *v2 = simdLoad( base + align * offset[2] );
-    *v3 = simdLoad( base + align * offset[3] );
-
-    __vector float t0 = vec_mergeh(v0->simdInternal_, v2->simdInternal_);
-    __vector float t1 = vec_mergel(v0->simdInternal_, v2->simdInternal_);
-    __vector float t2 = vec_mergeh(v1->simdInternal_, v3->simdInternal_);
-    __vector float t3 = vec_mergel(v1->simdInternal_, v3->simdInternal_);
+    __vector float l0, l1, l2, l3;
+
+    l0 = simdLoad( base + align * offset[0] ).simdInternal_;
+    l1 = simdLoad( base + align * offset[1] ).simdInternal_;
+    l2 = simdLoad( base + align * offset[2] ).simdInternal_;
+    l3 = simdLoad( base + align * offset[3] ).simdInternal_;
+
+    __vector float t0 = vec_mergeh(l0, l2);
+    __vector float t1 = vec_mergel(l0, l2);
+    __vector float t2 = vec_mergeh(l1, l3);
+    __vector float t3 = vec_mergel(l1, l3);
     v0->simdInternal_ = vec_mergeh(t0, t2);
     v1->simdInternal_ = vec_mergel(t0, t2);
     v2->simdInternal_ = vec_mergeh(t1, t3);
@@ -316,6 +318,9 @@
     triplets2->simdInternal_ = vec_perm(scalar.simdInternal_, t1, perm2);
 }
 
+/* TODO In debug mode, xlc 13.1.5 seems to overwrite v0 on the stack,
+   leading to segfaults. Possibly the calling convention doesn't
+   implement __vector int correctly. Release mode is OK. gcc is OK. */
 template <int align>
 static inline void gmx_simdcall
 gatherLoadBySimdIntTranspose(const float *  base,
diff -Nru gromacs-2016.2/src/gromacs/simd/tests/simd_math.cpp gromacs-2016.3/src/gromacs/simd/tests/simd_math.cpp
--- gromacs-2016.2/src/gromacs/simd/tests/simd_math.cpp	2016-07-09 00:55:39.000000000 +0000
+++ gromacs-2016.3/src/gromacs/simd/tests/simd_math.cpp	2017-03-13 17:22:33.000000000 +0000
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -439,8 +439,9 @@
     GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom1R(std::atan2(1.0, 0.0)), atan2(rSimd_1_2_3, setZero()));
     GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom1R(std::atan2(0.0, -1.0)), atan2(setZero(), rSimd_m1_m2_m3));
     GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom1R(std::atan2(-1.0, 0.0)), atan2(rSimd_m1_m2_m3, setZero()));
-    // degenerate value (origin) should return 0.0
-    GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom1R(std::atan2(0.0, 0.0)), atan2(setSimdRealFrom3R(0.0, 0.0, 0.0), setZero()));
+    // degenerate value (origin) should return 0.0. At least IBM xlc 13.1.5 gets the reference
+    // value wrong (-nan) at -O3 optimization, so we compare to the correct value (0.0) instead.
+    GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom1R(0.0), atan2(setSimdRealFrom3R(0.0, 0.0, 0.0), setZero()));
 }
 
 /*! \brief Evaluate reference version of PME force correction. */
@@ -691,8 +692,9 @@
     GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom1R(std::atan2(1.0, 0.0)), atan2SingleAccuracy(rSimd_1_2_3, setZero()));
     GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom1R(std::atan2(0.0, -1.0)), atan2SingleAccuracy(setZero(), rSimd_m1_m2_m3));
     GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom1R(std::atan2(-1.0, 0.0)), atan2SingleAccuracy(rSimd_m1_m2_m3, setZero()));
-    // degenerate value (origin) should return 0.0
-    GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom1R(std::atan2(0.0, 0.0)), atan2SingleAccuracy(setSimdRealFrom3R(0.0, 0.0, 0.0), setZero()));
+    // degenerate value (origin) should return 0.0. At least IBM xlc 13.1.5 gets the reference
+    // value wrong (-nan) at -O3 optimization, so we compare to the correct value (0.0) instead.
+    GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom1R(0.0), atan2SingleAccuracy(setSimdRealFrom3R(0.0, 0.0, 0.0), setZero()));
 }
 
 TEST_F(SimdMathTest, pmeForceCorrectionSingleAccuracy)
diff -Nru gromacs-2016.2/src/gromacs/utility/binaryinformation.cpp gromacs-2016.3/src/gromacs/utility/binaryinformation.cpp
--- gromacs-2016.2/src/gromacs/utility/binaryinformation.cpp	2016-07-09 00:55:39.000000000 +0000
+++ gromacs-2016.3/src/gromacs/utility/binaryinformation.cpp	2017-03-13 17:22:33.000000000 +0000
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -135,7 +135,7 @@
     };
     static const char * const CopyrightText[] = {
         "Copyright (c) 1991-2000, University of Groningen, The Netherlands.",
-        "Copyright (c) 2001-2015, The GROMACS development team at",
+        "Copyright (c) 2001-2017, The GROMACS development team at",
         "Uppsala University, Stockholm University and",
         "the Royal Institute of Technology, Sweden.",
         "check out http://www.gromacs.org for more information."
diff -Nru gromacs-2016.2/src/programs/mdrun/md.cpp gromacs-2016.3/src/programs/mdrun/md.cpp
--- gromacs-2016.2/src/programs/mdrun/md.cpp	2017-02-05 20:30:25.000000000 +0000
+++ gromacs-2016.3/src/programs/mdrun/md.cpp	2017-03-13 17:22:33.000000000 +0000
@@ -1193,8 +1193,15 @@
                     m_add(force_vir, shake_vir, total_vir);     /* we need the un-dispersion corrected total vir here */
                     trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ2);
 
-                    copy_mat(shake_vir, state->svir_prev);
-                    copy_mat(force_vir, state->fvir_prev);
+                    /* TODO This is only needed when we're about to write
+                     * a checkpoint, because we use it after the restart
+                     * (in a kludge?). But what should we be doing if
+                     * startingFromCheckpoint or bInitStep are true? */
+                    if (inputrecNptTrotter(ir) || inputrecNphTrotter(ir))
+                    {
+                        copy_mat(shake_vir, state->svir_prev);
+                        copy_mat(force_vir, state->fvir_prev);
+                    }
                     if (inputrecNvtTrotter(ir) && ir->eI == eiVV)
                     {
                         /* update temperature and kinetic energy now that step is over - this is the v(t+dt) point */
@@ -1272,7 +1279,7 @@
         bIMDstep = do_IMD(ir->bIMD, step, cr, bNS, state->box, state->x, ir, t, wcycle);
 
         /* kludge -- virial is lost with restart for MTTK NPT control. Must reload (saved earlier). */
-        if (startingFromCheckpoint && bTrotter)
+        if (startingFromCheckpoint && (inputrecNptTrotter(ir) || inputrecNphTrotter(ir)))
         {
             copy_mat(state->svir_prev, shake_vir);
             copy_mat(state->fvir_prev, force_vir);
diff -Nru gromacs-2016.2/src/testutils/CMakeLists.txt gromacs-2016.3/src/testutils/CMakeLists.txt
--- gromacs-2016.2/src/testutils/CMakeLists.txt	2016-12-06 18:53:27.000000000 +0000
+++ gromacs-2016.3/src/testutils/CMakeLists.txt	2017-03-13 17:22:33.000000000 +0000
@@ -1,7 +1,7 @@
 #
 # This file is part of the GROMACS molecular simulation package.
 #
-# Copyright (c) 2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -35,6 +35,7 @@
 include_directories(BEFORE SYSTEM ${GMOCK_INCLUDE_DIRS})
 set(TESTUTILS_SOURCES
     cmdlinetest.cpp
+    conftest.cpp
     integrationtests.cpp
     interactivetest.cpp
     mpi-printer.cpp
diff -Nru gromacs-2016.2/src/testutils/conftest.cpp gromacs-2016.3/src/testutils/conftest.cpp
--- gromacs-2016.2/src/testutils/conftest.cpp	1970-01-01 00:00:00.000000000 +0000
+++ gromacs-2016.3/src/testutils/conftest.cpp	2017-03-13 17:22:33.000000000 +0000
@@ -0,0 +1,106 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements routine to check the content of conf files.
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \ingroup module_testutils
+ */
+#include "gmxpre.h"
+
+#include "conftest.h"
+
+#include <cstdio>
+#include <cstdlib>
+
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/textstream.h"
+
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+#include "testutils/textblockmatchers.h"
+
+namespace gmx
+{
+
+namespace test
+{
+
+namespace
+{
+
+class ConfMatcher : public ITextBlockMatcher
+{
+    public:
+        explicit ConfMatcher(const ConfMatchSettings &settings) : settings_(settings)
+        {
+        }
+
+        virtual void checkStream(TextInputStream      *stream,
+                                 TestReferenceChecker *checker)
+        {
+            checkConfFile(stream, checker, settings_);
+        }
+    private:
+        ConfMatchSettings settings_;
+};
+
+}       // namespace
+
+void checkConfFile(TextInputStream         *input,
+                   TestReferenceChecker    *checker,
+                   const ConfMatchSettings  &)
+{
+
+    TestReferenceChecker groChecker(checker->checkCompound("GroFile", "Header"));
+    // Just check the first two lines of the output file
+    std::string          line;
+    EXPECT_TRUE(input->readLine(&line));
+    line = stripSuffixIfPresent(line, "\n");
+    groChecker.checkString(line, "Title");
+    EXPECT_TRUE(input->readLine(&line));
+    line = stripSuffixIfPresent(line, "\n");
+    groChecker.checkInteger(std::atoi(line.c_str()), "Number of atoms");
+}
+
+TextBlockMatcherPointer ConfMatch::createMatcher() const
+{
+    return TextBlockMatcherPointer(new ConfMatcher(settings_));
+}
+
+} // namespace test
+} // namespace gmx
diff -Nru gromacs-2016.2/src/testutils/conftest.h gromacs-2016.3/src/testutils/conftest.h
--- gromacs-2016.2/src/testutils/conftest.h	1970-01-01 00:00:00.000000000 +0000
+++ gromacs-2016.3/src/testutils/conftest.h	2017-03-13 17:22:33.000000000 +0000
@@ -0,0 +1,114 @@
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares function to add the content of a conf file to a checker.
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \inlibraryapi
+ * \ingroup module_testutils
+ */
+#ifndef GMX_TESTUTILS_CONFTEST_H
+#define GMX_TESTUTILS_CONFTEST_H
+
+#include <string>
+
+#include "testutils/testasserts.h"
+#include "testutils/textblockmatchers.h"
+
+namespace gmx
+{
+
+class TextInputStream;
+
+namespace test
+{
+
+class TestReferenceChecker;
+
+struct ConfMatchSettings
+{
+    ConfMatchSettings() : tolerance(defaultRealTolerance())
+    {
+    }
+
+    FloatingPointTolerance  tolerance;
+};
+
+/*! \brief
+ * Adds content of a gro file to TestReferenceChecker object.
+ *
+ * \param[in] input       Stream that provides the gro content.
+ * \param[in,out] checker Checker to use.
+ * \param[in] settings    Settings to use for matching.
+ *
+ * Parses a gro file from the input stream, and checks the contents against
+ * reference data (only first two lines for now).
+ *
+ * \see ConfMatch
+ */
+void checkConfFile(TextInputStream         *input,
+                   TestReferenceChecker    *checker,
+                   const ConfMatchSettings &settings);
+
+/*! \libinternal \brief
+ * Match the contents as an gro file.
+ *
+ * \see checkGroFile()
+ *
+ * \inlibraryapi
+ * \ingroup module_testutils
+ */
+class ConfMatch : public ITextBlockMatcherSettings
+{
+    public:
+        //! Sets the tolerance for matching floating point values.
+        ConfMatch &tolerance(const FloatingPointTolerance &tolerance)
+        {
+            settings_.tolerance = tolerance;
+            return *this;
+        }
+
+        virtual TextBlockMatcherPointer createMatcher() const;
+
+    private:
+        ConfMatchSettings  settings_;
+};
+
+} // namespace test
+
+} // namespace gmx
+
+#endif