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

New upstream version 2018.1

parent 524c0449
......@@ -5,7 +5,7 @@ Installation guide
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.
......@@ -28,8 +28,8 @@ Quick and dirty installation
Or, as a sequence of commands to execute:
tar xfz gromacs-2018.tar.gz
cd gromacs-2018
tar xfz gromacs-2018.1.tar.gz
cd gromacs-2018.1
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
......@@ -153,7 +153,7 @@ offer competitive performance. We recommend against PGI because the
performance with C++ is very bad.
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.
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
code you want to build. For example, download the source tarball and
use
tar xfz gromacs-2018.tgz
cd gromacs-2018
tar xfz gromacs-2018.1.tgz
cd gromacs-2018.1
mkdir build-gromacs
cd build-gromacs
cmake ..
......@@ -992,10 +992,11 @@ The simplest way to run the checks is to build GROMACS with
"-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-2018.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 please read on.
http://gerrit.gromacs.org/download/regressiontests-2018.1.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
please read on.
The regression tests are also available from the download section.
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
# Test clang + OpenMP
clang-5 openmp simd=avx_128_fma npme=1 nranks=2 mpi
# Test non-default use of mdrun -gpu_id
# Test SSE2 SIMD
# 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
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
# Add SIMD + OpenMP + CUDA asan 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
# Test thread-MPI with CUDA
# Test cmake version from before new FindCUDA support (in 3.8)
# 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 with ThreadSanitizer (compiled without OpenMP, even though
......@@ -62,11 +62,6 @@ clang-5 no-openmp asan
# Test newest supported MSVC on Windows
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 icc without SIMD in double precision in release mode
# Test MKL
......@@ -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
# 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)
# Test hwloc support
# Test newest supported LTS Ubuntu
......
#!/usr/bin/python
#!/usr/bin/env python2
#
# 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,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
......
#
# 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,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
......@@ -50,7 +50,7 @@ endfunction ()
if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS "4.0" AND
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 ${CMAKE_CXX_COMPILER_VERSION} for CUDA is only compatible with CUDA version <=8.0")
endif()
if (GMX_CUDA_TARGET_COMPUTE)
......@@ -64,18 +64,24 @@ if (GMX_CUDA_TARGET_SM)
list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_${_target}")
endforeach()
else()
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_35")
# 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_52")
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_61")
endif()
# TODO: test CUDA 9.0 and figure out which clang releases support it
# and the sm_70 arch.
if (NOT CUDA_VERSION VERSION_LESS 9.0)
list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_70")
endif()
endif()
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)")
......
......@@ -186,7 +186,7 @@
# 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 2018)
set(GMX_VERSION_PATCH 0)
set(GMX_VERSION_PATCH 1)
# 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
......@@ -203,7 +203,7 @@ set(GMX_VERSION_SUFFIX "")
# code being able to dynamically link with a version of libgromacs
# that might not work.
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)
#####################################################################
......@@ -226,7 +226,7 @@ endif()
set(REGRESSIONTEST_VERSION "${GMX_VERSION_STRING}")
set(REGRESSIONTEST_BRANCH "refs/heads/release-2018")
set(REGRESSIONTEST_MD5SUM "5a609bea6b6777072063be9e665121ef" CACHE INTERNAL "MD5 sum of the regressiontests tarball")
set(REGRESSIONTEST_MD5SUM "1a94916e2cf90e34fddb3514a65e0154" CACHE INTERNAL "MD5 sum of the regressiontests tarball")
math(EXPR GMX_VERSION_NUMERIC
"${GMX_VERSION_MAJOR}*10000 + ${GMX_VERSION_PATCH}")
......
......@@ -125,13 +125,28 @@ if (SPHINX_FOUND)
fragments/doxygen-links.rst
install-guide/index.rst
release-notes/index.rst
release-notes/features.rst
release-notes/performance.rst
release-notes/tools.rst
release-notes/bugs-fixed.rst
release-notes/removed-features.rst
release-notes/portability.rst
release-notes/miscellaneous.rst
release-notes/2018/2018.1.rst
release-notes/2018/major/highlights.rst
release-notes/2018/major/features.rst
release-notes/2018/major/performance.rst
release-notes/2018/major/tools.rst
release-notes/2018/major/bugs-fixed.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/cutoff-schemes.rst
user-guide/getting-started.rst
......
#!/usr/bin/python
#!/usr/bin/env python2
#
# 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,
# and including many others, as listed in the AUTHORS file in the
# 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.
#
# 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,
# and including many others, as listed in the AUTHORS file in the
# 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.
#
# 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,
# and including many others, as listed in the AUTHORS file in the
# 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.
#
# 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,
# and including many others, as listed in the AUTHORS file in the
# 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.
#
# 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,
# and including many others, as listed in the AUTHORS file in the
# 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.
#
# 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,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
......
.\" 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
gmx-anadock \- Cluster structures from Autodock runs
.
......
.\" 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
gmx-anaeig \- Analyze eigenvectors/normal modes
.
......
.\" 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
gmx-analyze \- Analyze data sets
.
......
.\" 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
gmx-angle \- Calculate distributions and correlations for angles and dihedrals
.
......
.\" 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
gmx-awh \- Extract data from an accelerated weight histogram (AWH) run
.
......
.\" 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
gmx-bar \- Calculate free energy difference estimates through Bennett's acceptance ratio
.
......
.\" 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
gmx-bundle \- Analyze bundles of axes, e.g., helices
.
......
.\" 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
gmx-check \- Check and compare files
.
......
.\" 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
gmx-chi \- Calculate everything you want to know about chi and other dihedrals
.
......
.\" 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
gmx-cluster \- Cluster structures
.
......
.\" 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
gmx-clustsize \- Calculate size distributions of atomic clusters
.
......
.\" 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
gmx-confrms \- Fit two structures and calculates the RMSD
.
......
.\" 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
gmx-convert-tpr \- Make a modifed run-input file
.
......
.\" 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
gmx-covar \- Calculate and diagonalize the covariance matrix
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CURRENT" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-CURRENT" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-current \- Calculate dielectric constants and current autocorrelation function
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DENSITY" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-DENSITY" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-density \- Calculate the density of the system
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DENSMAP" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-DENSMAP" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-densmap \- Calculate 2D planar or axial-radial density maps
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DENSORDER" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-DENSORDER" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-densorder \- Calculate surface fluctuations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DIELECTRIC" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-DIELECTRIC" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-dielectric \- Calculate frequency dependent dielectric constants
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DIPOLES" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-DIPOLES" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-dipoles \- Compute the total dipole plus fluctuations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DISRE" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-DISRE" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-disre \- Analyze distance restraints
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DISTANCE" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-DISTANCE" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-distance \- Calculate distances between pairs of positions
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DO_DSSP" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-DO_DSSP" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-do_dssp \- Assign secondary structure and calculate solvent accessible surface area
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DOS" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-DOS" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-dos \- Analyze density of states and properties based on that
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DUMP" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-DUMP" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-dump \- Make binary files human readable
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DYECOUPL" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-DYECOUPL" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-dyecoupl \- Extract dye dynamics from trajectories
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DYNDOM" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-DYNDOM" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-dyndom \- Interpolate and extrapolate structure rotations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-EDITCONF" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-EDITCONF" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-editconf \- Convert and manipulates structure files
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ENECONV" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-ENECONV" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-eneconv \- Convert energy files
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ENEMAT" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-ENEMAT" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-enemat \- Extract an energy matrix from an energy file
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ENERGY" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-ENERGY" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-energy \- Writes energies to xvg files and display averages
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-FILTER" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-FILTER" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-filter \- Frequency filter trajectories, useful for making smooth movies
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-FREEVOLUME" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-FREEVOLUME" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-freevolume \- Calculate free volume
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-GANGLE" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-GANGLE" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-gangle \- Calculate angles
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-GENCONF" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-GENCONF" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-genconf \- Multiply a conformation in 'random' orientations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-GENION" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-GENION" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-genion \- Generate monoatomic ions on energetically favorable positions
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-GENRESTR" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-GENRESTR" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-genrestr \- Generate position restraints or distance restraints for index groups
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-GROMPP" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-GROMPP" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-grompp \- Make a run input file
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.TH "GMX-GYRATE" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-GYRATE" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-gyrate \- Calculate the radius of gyration
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.TH "GMX-H2ORDER" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-H2ORDER" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-h2order \- Compute the orientation of water molecules
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.TH "GMX-HBOND" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-HBOND" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-hbond \- Compute and analyze hydrogen bonds
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.TH "GMX-HELIX" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-HELIX" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-helix \- Calculate basic properties of alpha helices
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.TH "GMX-HELIXORIENT" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-HELIXORIENT" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-helixorient \- Calculate local pitch/bending/rotation/orientation inside helices
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.TH "GMX-HELP" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-HELP" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-help \- Print help information
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.TH "GMX-HYDORDER" "1" "Jan 11, 2018" "2018" "GROMACS"
.TH "GMX-HYDORDER" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.SH NAME
gmx-hydorder \- Compute tetrahedrality parameters around a given atom
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.TH "GMX-INSERT-MOLECULES" "1" "Jan 11, 2018" "2018" "GROMACS"