Commit 1d960618 authored by Nicholas Breen's avatar Nicholas Breen

New upstream version 2018.1

parent 524c0449
...@@ -5,7 +5,7 @@ Installation guide ...@@ -5,7 +5,7 @@ Installation guide
Introduction to building GROMACS Introduction to building GROMACS
================================ ================================
These instructions pertain to building GROMACS 2018. You might also These instructions pertain to building GROMACS 2018.1. You might also
want to check the up-to-date installation instructions. want to check the up-to-date installation instructions.
...@@ -28,8 +28,8 @@ Quick and dirty installation ...@@ -28,8 +28,8 @@ Quick and dirty installation
Or, as a sequence of commands to execute: Or, as a sequence of commands to execute:
tar xfz gromacs-2018.tar.gz tar xfz gromacs-2018.1.tar.gz
cd gromacs-2018 cd gromacs-2018.1
mkdir build mkdir build
cd build cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
...@@ -153,7 +153,7 @@ offer competitive performance. We recommend against PGI because the ...@@ -153,7 +153,7 @@ offer competitive performance. We recommend against PGI because the
performance with C++ is very bad. performance with C++ is very bad.
The xlc compiler is not supported and has not been tested on POWER The xlc compiler is not supported and has not been tested on POWER
architectures for GROMACS-2018. We recommend to use the gcc compiler architectures for GROMACS-2018.1. We recommend to use the gcc compiler
instead, as it is being extensively tested. instead, as it is being extensively tested.
You may also need the most recent version of other compiler toolchain You may also need the most recent version of other compiler toolchain
...@@ -417,8 +417,8 @@ the name of the directory containing the "CMakeLists.txt" file of the ...@@ -417,8 +417,8 @@ the name of the directory containing the "CMakeLists.txt" file of the
code you want to build. For example, download the source tarball and code you want to build. For example, download the source tarball and
use use
tar xfz gromacs-2018.tgz tar xfz gromacs-2018.1.tgz
cd gromacs-2018 cd gromacs-2018.1
mkdir build-gromacs mkdir build-gromacs
cd build-gromacs cd build-gromacs
cmake .. cmake ..
...@@ -992,10 +992,11 @@ The simplest way to run the checks is to build GROMACS with ...@@ -992,10 +992,11 @@ The simplest way to run the checks is to build GROMACS with
"-DREGRESSIONTEST_DOWNLOAD", and run "make check". GROMACS will "-DREGRESSIONTEST_DOWNLOAD", and run "make check". GROMACS will
automatically download and run the tests for you. Alternatively, you automatically download and run the tests for you. Alternatively, you
can download and unpack the GROMACS regression test suite can download and unpack the GROMACS regression test suite
http://gerrit.gromacs.org/download/regressiontests-2018.tar.gz tarball http://gerrit.gromacs.org/download/regressiontests-2018.1.tar.gz
yourself and use the advanced "cmake" option "REGRESSIONTEST_PATH" to tarball yourself and use the advanced "cmake" option
specify the path to the unpacked tarball, which will then be used for "REGRESSIONTEST_PATH" to specify the path to the unpacked tarball,
testing. If the above does not work, then please read on. which will then be used for testing. If the above does not work, then
please read on.
The regression tests are also available from the download section. The regression tests are also available from the download section.
Once you have downloaded them, unpack the tarball, source "GMXRC" as Once you have downloaded them, unpack the tarball, source "GMXRC" as
......
...@@ -48,14 +48,19 @@ clang-4 simd=sse4.1 openmp nranks=1 gpu cuda-8.0 clang_cuda ...@@ -48,14 +48,19 @@ clang-4 simd=sse4.1 openmp nranks=1 gpu cuda-8.0 clang_cuda
# Test clang + OpenMP # Test clang + OpenMP
clang-5 openmp simd=avx_128_fma npme=1 nranks=2 mpi clang-5 openmp simd=avx_128_fma npme=1 nranks=2 mpi
# Test non-default use of mdrun -gpu_id
# Test SSE2 SIMD # Test SSE2 SIMD
# Test CMAKE_BUILD_TYPE=Release # Test CMAKE_BUILD_TYPE=Release
gcc-4.8 gpu npme=1 nranks=2 gpu_id=2 cuda-7.5 simd=sse2 release gcc-4.8 gpu npme=1 nranks=2 cuda-7.5 simd=sse2 release
# Test non-default use of mdrun -gpu_id
# Test GPU-sharing among 4 PP ranks # Test GPU-sharing among 4 PP ranks
gcc-5 gpu nranks=4 gpu_id=1 cuda-8.0 release-with-assert gcc-5 gpu nranks=4 gpu_id=1 cuda-8.0 release-with-assert
# Test oldest supported icc
# Test icc on Windows
# Test icc with SIMD in mixed precision in release mode
icc-16 msvc-2015 fftpack simd=avx2_256 release
# TODO # TODO
# Add SIMD + OpenMP + CUDA asan build # Add SIMD + OpenMP + CUDA asan build
# Add OpenMP + CUDA + device sharing TSAN build # Add OpenMP + CUDA + device sharing TSAN build
......
...@@ -27,7 +27,7 @@ gcc-4.8 gpu cuda-6.5 cmake-3.8.1 mpi npme=1 nranks=2 openmp ...@@ -27,7 +27,7 @@ gcc-4.8 gpu cuda-6.5 cmake-3.8.1 mpi npme=1 nranks=2 openmp
# Test thread-MPI with CUDA # Test thread-MPI with CUDA
# Test cmake version from before new FindCUDA support (in 3.8) # Test cmake version from before new FindCUDA support (in 3.8)
# Test SIMD implementation of pair search for GPU code-path # Test SIMD implementation of pair search for GPU code-path
gcc-5 gpu cuda-8.0 thread-mpi openmp cmake-3.6.1 release-with-assert simd=avx2_256 gcc-6 gpu cuda-9.0 thread-mpi openmp cmake-3.6.1 release-with-assert simd=avx2_256
# Test newest cmake at time of release # Test newest cmake at time of release
# Test with ThreadSanitizer (compiled without OpenMP, even though # Test with ThreadSanitizer (compiled without OpenMP, even though
...@@ -62,11 +62,6 @@ clang-5 no-openmp asan ...@@ -62,11 +62,6 @@ clang-5 no-openmp asan
# Test newest supported MSVC on Windows # Test newest supported MSVC on Windows
msvc-2015 openmp release-with-assert msvc-2015 openmp release-with-assert
# Test oldest supported icc
# Test icc on Windows
# Test icc with SIMD in mixed precision in release mode
icc-16 msvc-2015 fftpack simd=avx2_256 release
# Test newest icc at the time of release # Test newest icc at the time of release
# Test icc without SIMD in double precision in release mode # Test icc without SIMD in double precision in release mode
# Test MKL # Test MKL
...@@ -85,7 +80,6 @@ icc-18 openmp opencl cuda-7.5 mpi release simd=avx2_256 ...@@ -85,7 +80,6 @@ icc-18 openmp opencl cuda-7.5 mpi release simd=avx2_256
gcc-5 openmp simd=avx_128_fma opencl amdappsdk-3.0 gcc-5 openmp simd=avx_128_fma opencl amdappsdk-3.0
# TODO # TODO
# Add support for CUDA 9.0
# Add OpenMP support to ASAN build (but libomp.so in clang-4 reports leaks, so might need a suitable build or suppression) # Add OpenMP support to ASAN build (but libomp.so in clang-4 reports leaks, so might need a suitable build or suppression)
# Test hwloc support # Test hwloc support
# Test newest supported LTS Ubuntu # Test newest supported LTS Ubuntu
......
#!/usr/bin/python #!/usr/bin/env python2
# #
# This file is part of the GROMACS molecular simulation package. # This file is part of the GROMACS molecular simulation package.
# #
# Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by # Copyright (c) 2013,2014,2015,2016,2018, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the # and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org. # top-level source directory and at http://www.gromacs.org.
......
# #
# This file is part of the GROMACS molecular simulation package. # This file is part of the GROMACS molecular simulation package.
# #
# Copyright (c) 2017, by the GROMACS development team, led by # Copyright (c) 2017,2018, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the # and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org. # top-level source directory and at http://www.gromacs.org.
...@@ -50,7 +50,7 @@ endfunction () ...@@ -50,7 +50,7 @@ endfunction ()
if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS "4.0" AND if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS "4.0" AND
NOT CUDA_VERSION VERSION_LESS "8.0") NOT CUDA_VERSION VERSION_LESS "8.0")
message(FATAL_ERROR "clang ${CMAKE_CXX_COMPILER_VERSION} for CUDA is only compatible with CUDA version <8.0") message(FATAL_ERROR "clang ${CMAKE_CXX_COMPILER_VERSION} for CUDA is only compatible with CUDA version <=8.0")
endif() endif()
if (GMX_CUDA_TARGET_COMPUTE) if (GMX_CUDA_TARGET_COMPUTE)
...@@ -64,18 +64,24 @@ if (GMX_CUDA_TARGET_SM) ...@@ -64,18 +64,24 @@ if (GMX_CUDA_TARGET_SM)
list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_${_target}") list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_${_target}")
endforeach() endforeach()
else() else()
list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_20") if(CUDA_VERSION VERSION_LESS "9.00") # < 9.0
list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_20")
endif()
list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_30") list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_30")
list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_35") list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_35")
list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_37") # clang 6.0 + CUDA 9.0 seems to have issues generating code for sm_37
if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 6.0 OR CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 6.0.999)
list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_37")
endif()
list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_50") list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_50")
list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_52") list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_52")
if (NOT CUDA_VERSION VERSION_LESS 8.0) if (NOT CUDA_VERSION VERSION_LESS 8.0)
list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_60") list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_60")
list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_61") list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_61")
endif() endif()
# TODO: test CUDA 9.0 and figure out which clang releases support it if (NOT CUDA_VERSION VERSION_LESS 9.0)
# and the sm_70 arch. list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_70")
endif()
endif() endif()
if (GMX_CUDA_TARGET_SM) if (GMX_CUDA_TARGET_SM)
set_property(CACHE GMX_CUDA_TARGET_SM PROPERTY HELPSTRING "List of CUDA GPU architecture codes to compile for (without the sm_ prefix)") set_property(CACHE GMX_CUDA_TARGET_SM PROPERTY HELPSTRING "List of CUDA GPU architecture codes to compile for (without the sm_ prefix)")
......
...@@ -186,7 +186,7 @@ ...@@ -186,7 +186,7 @@
# The GROMACS convention is that these are the version number of the next # The GROMACS convention is that these are the version number of the next
# release that is going to be made from this branch. # release that is going to be made from this branch.
set(GMX_VERSION_MAJOR 2018) set(GMX_VERSION_MAJOR 2018)
set(GMX_VERSION_PATCH 0) set(GMX_VERSION_PATCH 1)
# The suffix, on the other hand, is used mainly for betas and release # The suffix, on the other hand, is used mainly for betas and release
# candidates, where it signifies the most recent such release from # candidates, where it signifies the most recent such release from
# this branch; it will be empty before the first such release, as well # this branch; it will be empty before the first such release, as well
...@@ -203,7 +203,7 @@ set(GMX_VERSION_SUFFIX "") ...@@ -203,7 +203,7 @@ set(GMX_VERSION_SUFFIX "")
# code being able to dynamically link with a version of libgromacs # code being able to dynamically link with a version of libgromacs
# that might not work. # that might not work.
set(LIBRARY_SOVERSION_MAJOR 3) set(LIBRARY_SOVERSION_MAJOR 3)
set(LIBRARY_SOVERSION_MINOR 0) set(LIBRARY_SOVERSION_MINOR 1)
set(LIBRARY_VERSION ${LIBRARY_SOVERSION_MAJOR}.${LIBRARY_SOVERSION_MINOR}.0) set(LIBRARY_VERSION ${LIBRARY_SOVERSION_MAJOR}.${LIBRARY_SOVERSION_MINOR}.0)
##################################################################### #####################################################################
...@@ -226,7 +226,7 @@ endif() ...@@ -226,7 +226,7 @@ endif()
set(REGRESSIONTEST_VERSION "${GMX_VERSION_STRING}") set(REGRESSIONTEST_VERSION "${GMX_VERSION_STRING}")
set(REGRESSIONTEST_BRANCH "refs/heads/release-2018") set(REGRESSIONTEST_BRANCH "refs/heads/release-2018")
set(REGRESSIONTEST_MD5SUM "5a609bea6b6777072063be9e665121ef" CACHE INTERNAL "MD5 sum of the regressiontests tarball") set(REGRESSIONTEST_MD5SUM "1a94916e2cf90e34fddb3514a65e0154" CACHE INTERNAL "MD5 sum of the regressiontests tarball")
math(EXPR GMX_VERSION_NUMERIC math(EXPR GMX_VERSION_NUMERIC
"${GMX_VERSION_MAJOR}*10000 + ${GMX_VERSION_PATCH}") "${GMX_VERSION_MAJOR}*10000 + ${GMX_VERSION_PATCH}")
......
...@@ -125,13 +125,28 @@ if (SPHINX_FOUND) ...@@ -125,13 +125,28 @@ if (SPHINX_FOUND)
fragments/doxygen-links.rst fragments/doxygen-links.rst
install-guide/index.rst install-guide/index.rst
release-notes/index.rst release-notes/index.rst
release-notes/features.rst release-notes/2018/2018.1.rst
release-notes/performance.rst release-notes/2018/major/highlights.rst
release-notes/tools.rst release-notes/2018/major/features.rst
release-notes/bugs-fixed.rst release-notes/2018/major/performance.rst
release-notes/removed-features.rst release-notes/2018/major/tools.rst
release-notes/portability.rst release-notes/2018/major/bugs-fixed.rst
release-notes/miscellaneous.rst release-notes/2018/major/removed-features.rst
release-notes/2018/major/portability.rst
release-notes/2018/major/miscellaneous.rst
release-notes/2016/2016.5.rst
release-notes/2016/2016.4.rst
release-notes/2016/2016.3.rst
release-notes/2016/2016.2.rst
release-notes/2016/2016.1.rst
release-notes/2016/major/highlights.rst
release-notes/2016/major/new-features.rst
release-notes/2016/major/performance.rst
release-notes/2016/major/tools.rst
release-notes/2016/major/bugs-fixed.rst
release-notes/2016/major/removed-features.rst
release-notes/2016/major/miscellaneous.rst
release-notes/older/index.rst
user-guide/index.rst user-guide/index.rst
user-guide/cutoff-schemes.rst user-guide/cutoff-schemes.rst
user-guide/getting-started.rst user-guide/getting-started.rst
......
#!/usr/bin/python #!/usr/bin/env python2
# #
# This file is part of the GROMACS molecular simulation package. # This file is part of the GROMACS molecular simulation package.
# #
# Copyright (c) 2014,2015, by the GROMACS development team, led by # Copyright (c) 2014,2015,2018, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the # and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org. # top-level source directory and at http://www.gromacs.org.
......
#!/usr/bin/python #!/usr/bin/env python2
# #
# This file is part of the GROMACS molecular simulation package. # This file is part of the GROMACS molecular simulation package.
# #
# Copyright (c) 2014,2015,2016, by the GROMACS development team, led by # Copyright (c) 2014,2015,2016,2018, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the # and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org. # top-level source directory and at http://www.gromacs.org.
......
#!/usr/bin/python #!/usr/bin/env python2
# #
# This file is part of the GROMACS molecular simulation package. # This file is part of the GROMACS molecular simulation package.
# #
# Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by # Copyright (c) 2014,2015,2016,2017,2018, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the # and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org. # top-level source directory and at http://www.gromacs.org.
......
#!/usr/bin/python #!/usr/bin/env python2
# #
# This file is part of the GROMACS molecular simulation package. # This file is part of the GROMACS molecular simulation package.
# #
# Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by # Copyright (c) 2012,2013,2014,2015,2018, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the # and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org. # top-level source directory and at http://www.gromacs.org.
......
#!/usr/bin/python #!/usr/bin/env python2
# #
# This file is part of the GROMACS molecular simulation package. # This file is part of the GROMACS molecular simulation package.
# #
# Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by # Copyright (c) 2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the # and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org. # top-level source directory and at http://www.gromacs.org.
......
#!/usr/bin/python #!/usr/bin/env python2
# #
# This file is part of the GROMACS molecular simulation package. # This file is part of the GROMACS molecular simulation package.
# #
# Copyright (c) 2014, by the GROMACS development team, led by # Copyright (c) 2014,2018, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl, # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the # and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org. # top-level source directory and at http://www.gromacs.org.
......
.\" Man page generated from reStructuredText. .\" Man page generated from reStructuredText.
. .
.TH "GMX-ANADOCK" "1" "Jan 11, 2018" "2018" "GROMACS" .TH "GMX-ANADOCK" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME .SH NAME
gmx-anadock \- Cluster structures from Autodock runs gmx-anadock \- Cluster structures from Autodock runs
. .
......
.\" Man page generated from reStructuredText. .\" Man page generated from reStructuredText.
. .
.TH "GMX-ANAEIG" "1" "Jan 11, 2018" "2018" "GROMACS" .TH "GMX-ANAEIG" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME .SH NAME
gmx-anaeig \- Analyze eigenvectors/normal modes gmx-anaeig \- Analyze eigenvectors/normal modes
. .
......
.\" Man page generated from reStructuredText. .\" Man page generated from reStructuredText.
. .
.TH "GMX-ANALYZE" "1" "Jan 11, 2018" "2018" "GROMACS" .TH "GMX-ANALYZE" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME .SH NAME
gmx-analyze \- Analyze data sets gmx-analyze \- Analyze data sets
. .
......
.\" Man page generated from reStructuredText. .\" Man page generated from reStructuredText.
. .
.TH "GMX-ANGLE" "1" "Jan 11, 2018" "2018" "GROMACS" .TH "GMX-ANGLE" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME .SH NAME
gmx-angle \- Calculate distributions and correlations for angles and dihedrals gmx-angle \- Calculate distributions and correlations for angles and dihedrals
. .
......
.\" Man page generated from reStructuredText. .\" Man page generated from reStructuredText.
. .
.TH "GMX-AWH" "1" "Jan 11, 2018" "2018" "GROMACS" .TH "GMX-AWH" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME .SH NAME
gmx-awh \- Extract data from an accelerated weight histogram (AWH) run gmx-awh \- Extract data from an accelerated weight histogram (AWH) run
. .
......
.\" Man page generated from reStructuredText. .\" Man page generated from reStructuredText.
. .
.TH "GMX-BAR" "1" "Jan 11, 2018" "2018" "GROMACS" .TH "GMX-BAR" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME .SH NAME
gmx-bar \- Calculate free energy difference estimates through Bennett's acceptance ratio gmx-bar \- Calculate free energy difference estimates through Bennett's acceptance ratio
. .
......
.\" Man page generated from reStructuredText. .\" Man page generated from reStructuredText.
. .
.TH "GMX-BUNDLE" "1" "Jan 11, 2018" "2018" "GROMACS" .TH "GMX-BUNDLE" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME .SH NAME
gmx-bundle \- Analyze bundles of axes, e.g., helices gmx-bundle \- Analyze bundles of axes, e.g., helices
. .
......
.\" Man page generated from reStructuredText. .\" Man page generated from reStructuredText.
. .
.TH "GMX-CHECK" "1" "Jan 11, 2018" "2018" "GROMACS" .TH "GMX-CHECK" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME .SH NAME
gmx-check \- Check and compare files gmx-check \- Check and compare files
. .
......
.\" Man page generated from reStructuredText. .\" Man page generated from reStructuredText.
. .
.TH "GMX-CHI" "1" "Jan 11, 2018" "2018" "GROMACS" .TH "GMX-CHI" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME .SH NAME
gmx-chi \- Calculate everything you want to know about chi and other dihedrals gmx-chi \- Calculate everything you want to know about chi and other dihedrals
. .
......
.\" Man page generated from reStructuredText. .\" Man page generated from reStructuredText.
. .
.TH "GMX-CLUSTER" "1" "Jan 11, 2018" "2018" "GROMACS" .TH "GMX-CLUSTER" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME .SH NAME
gmx-cluster \- Cluster structures gmx-cluster \- Cluster structures
. .
......
.\" Man page generated from reStructuredText. .\" Man page generated from reStructuredText.
. .
.TH "GMX-CLUSTSIZE" "1" "Jan 11, 2018" "2018" "GROMACS" .TH "GMX-CLUSTSIZE" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME .SH NAME
gmx-clustsize \- Calculate size distributions of atomic clusters gmx-clustsize \- Calculate size distributions of atomic clusters
. .
......
.\" Man page generated from reStructuredText. .\" Man page generated from reStructuredText.
. .
.TH "GMX-CONFRMS" "1" "Jan 11, 2018" "2018" "GROMACS" .TH "GMX-CONFRMS" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME .SH NAME
gmx-confrms \- Fit two structures and calculates the RMSD gmx-confrms \- Fit two structures and calculates the RMSD
. .
......
.\" Man page generated from reStructuredText. .\" Man page generated from reStructuredText.
. .
.TH "GMX-CONVERT-TPR" "1" "Jan 11, 2018" "2018" "GROMACS" .TH "GMX-CONVERT-TPR" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME .SH NAME
gmx-convert-tpr \- Make a modifed run-input file gmx-convert-tpr \- Make a modifed run-input file
. .
......
.\" Man page generated from reStructuredText. .\" Man page generated from reStructuredText.
. .
.TH "GMX-COVAR" "1" "Jan 11, 2018" "2018" "GROMACS" .TH "GMX-COVAR" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME .SH NAME
gmx-covar \- Calculate and diagonalize the covariance matrix gmx-covar \- Calculate and diagonalize the covariance matrix
. .
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.TH "GMX-CURRENT" "1" "Jan 11, 2018" "2018" "GROMACS" .TH "GMX-CURRENT" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME .SH NAME
gmx-current \- Calculate dielectric constants and current autocorrelation function gmx-current \- Calculate dielectric constants and current autocorrelation function
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.TH "GMX-DENSITY" "1" "Jan 11, 2018" "2018" "GROMACS" .TH "GMX-DENSITY" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME .SH NAME
gmx-density \- Calculate the density of the system gmx-density \- Calculate the density of the system
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.TH "GMX-DENSMAP" "1" "Jan 11, 2018" "2018" "GROMACS" .TH "GMX-DENSMAP" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME .SH NAME
gmx-densmap \- Calculate 2D planar or axial-radial density maps gmx-densmap \- Calculate 2D planar or axial-radial density maps
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.TH "GMX-DENSORDER" "1" "Jan 11, 2018" "2018" "GROMACS" .TH "GMX-DENSORDER" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME .SH NAME
gmx-densorder \- Calculate surface fluctuations gmx-densorder \- Calculate surface fluctuations
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.TH "GMX-DIELECTRIC" "1" "Jan 11, 2018" "2018" "GROMACS" .TH "GMX-DIELECTRIC" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME .SH NAME
gmx-dielectric \- Calculate frequency dependent dielectric constants gmx-dielectric \- Calculate frequency dependent dielectric constants
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.TH "GMX-DIPOLES" "1" "Jan 11, 2018" "2018" "GROMACS" .TH "GMX-DIPOLES" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME .SH NAME
gmx-dipoles \- Compute the total dipole plus fluctuations gmx-dipoles \- Compute the total dipole plus fluctuations
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.TH "GMX-DISRE" "1" "Jan 11, 2018" "2018" "GROMACS" .TH "GMX-DISRE" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME .SH NAME
gmx-disre \- Analyze distance restraints gmx-disre \- Analyze distance restraints
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.TH "GMX-DISTANCE" "1" "Jan 11, 2018" "2018" "GROMACS" .TH "GMX-DISTANCE" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME .SH NAME
gmx-distance \- Calculate distances between pairs of positions gmx-distance \- Calculate distances between pairs of positions
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