Commit 044d75cd authored by Nicholas Breen's avatar Nicholas Breen

New upstream version 2019~beta3

parent c8d5e6b8
...@@ -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 2019-beta2. You might These instructions pertain to building GROMACS 2019-beta3. You might
also want to check the up-to-date installation instructions. also 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-2019-beta2.tar.gz tar xfz gromacs-2019-beta3.tar.gz
cd gromacs-2019-beta2 cd gromacs-2019-beta3
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
...@@ -166,7 +166,7 @@ offer competitive performance. We recommend against PGI because the ...@@ -166,7 +166,7 @@ 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-2019-beta2. We recommend to use the gcc architectures for GROMACS-2019-beta3. We recommend to use the gcc
compiler instead, as it is being extensively tested. compiler 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
...@@ -434,8 +434,8 @@ the name of the directory containing the "CMakeLists.txt" file of the ...@@ -434,8 +434,8 @@ 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-2019-beta2.tgz tar xfz gromacs-2019-beta3.tgz
cd gromacs-2019-beta2 cd gromacs-2019-beta3
mkdir build-gromacs mkdir build-gromacs
cd build-gromacs cd build-gromacs
cmake .. cmake ..
...@@ -799,7 +799,7 @@ gmxapi external API ...@@ -799,7 +799,7 @@ gmxapi external API
For dynamic linking builds and on non-Windows platforms, an extra For dynamic linking builds and on non-Windows platforms, an extra
library and headers are installed by setting "-DGMXAPI=ON" (default). library and headers are installed by setting "-DGMXAPI=ON" (default).
Build targets "gmxapi_cppdocs" and "gmxapi_cppdocs_dev" produce Build targets "gmxapi-cppdocs" and "gmxapi-cppdocs-dev" produce
documentation in "docs/api-user" and "docs/api-dev", respectively. For documentation in "docs/api-user" and "docs/api-dev", respectively. For
more project information and use cases, refer to the tracked Issue more project information and use cases, refer to the tracked Issue
2585, associated GitHub gmxapi projects, or DOI 2585, associated GitHub gmxapi projects, or DOI
...@@ -1022,7 +1022,7 @@ The simplest way to run the checks is to build GROMACS with ...@@ -1022,7 +1022,7 @@ 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-2019-beta2.tar.gz http://gerrit.gromacs.org/download/regressiontests-2019-beta3.tar.gz
tarball yourself and use the advanced "cmake" option tarball yourself and use the advanced "cmake" option
"REGRESSIONTEST_PATH" to specify the path to the unpacked tarball, "REGRESSIONTEST_PATH" to specify the path to the unpacked tarball,
which will then be used for testing. If the above does not work, then which will then be used for testing. If the above does not work, then
......
...@@ -11,7 +11,7 @@ ...@@ -11,7 +11,7 @@
# Test on ARM v7 # Test on ARM v7
# Test ARM_NEON SIMD # Test ARM_NEON SIMD
gcc-5 simd=ARM_NEON release-with-assert gcc-5 simd=ARM_NEON no-hwloc release-with-assert
# Test on ARM v8 # Test on ARM v8
# Test ARM_NEON_ASIMD SIMD # Test ARM_NEON_ASIMD SIMD
...@@ -67,7 +67,7 @@ icc-18 msvc-2017 fftpack simd=avx2_256 release ...@@ -67,7 +67,7 @@ icc-18 msvc-2017 fftpack simd=avx2_256 release
#gcc-7 armhpc-18.2 openmp simd=ARM_NEON_ASIMD release #gcc-7 armhpc-18.2 openmp simd=ARM_NEON_ASIMD release
# Test ARM HPC compier toolchain with armclang # Test ARM HPC compier toolchain with armclang
#armclang-18.2 armhpc-18.2 openmp simd=ARM_NEON_ASIMD release-with-assert armclang-18.4 armhpc-18.4 openmp simd=ARM_NEON_ASIMD release-with-assert
# TODO # TODO
# Add SIMD + OpenMP + CUDA asan build # Add SIMD + OpenMP + CUDA asan build
......
# #
# This file is part of the GROMACS molecular simulation package. # This file is part of the GROMACS molecular simulation package.
# #
# Copyright (c) 2015,2016,2017, by the GROMACS development team, led by # Copyright (c) 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.
...@@ -85,6 +85,7 @@ if(HWLOC_INCLUDE_DIRS) ...@@ -85,6 +85,7 @@ if(HWLOC_INCLUDE_DIRS)
# If we are not cross-compiling we try to use the hwloc-info program # If we are not cross-compiling we try to use the hwloc-info program
if(NOT CMAKE_CROSSCOMPILING) if(NOT CMAKE_CROSSCOMPILING)
find_program(HWLOC_INFO "hwloc-info") find_program(HWLOC_INFO "hwloc-info")
mark_as_advanced(HWLOC_INFO)
if(HWLOC_INFO) if(HWLOC_INFO)
execute_process(COMMAND ${HWLOC_INFO} "--version" execute_process(COMMAND ${HWLOC_INFO} "--version"
......
...@@ -50,8 +50,19 @@ if (SPHINX_EXECUTABLE AND NOT DEFINED SPHINX_EXECUTABLE_VERSION) ...@@ -50,8 +50,19 @@ if (SPHINX_EXECUTABLE AND NOT DEFINED SPHINX_EXECUTABLE_VERSION)
ERROR_QUIET ERROR_QUIET
OUTPUT_STRIP_TRAILING_WHITESPACE OUTPUT_STRIP_TRAILING_WHITESPACE
) )
string(REGEX REPLACE ".*build[ )]*" "" SPHINX_EXECUTABLE_VERSION "${SPHINX_VERSION_OUTPUT_VARIABLE}")
set(SPHINX_EXECUTABLE_VERSION "${SPHINX_EXECUTABLE_VERSION}" CACHE INTERNAL "Version of ${SPHINX_EXECUTABLE}") # Detect the sphinx version. First try to match the error message
# from old versions that didn't even support --version, then try
# to detect more modern sphinx versions. If nothing is found, then
# the cache variable is set to an empty value.
set(_version "")
if(SPHINX_VERSION_OUTPUT_VARIABLE MATCHES "Sphinx v([0-9\.]+)\n.*")
set(_version ${CMAKE_MATCH_1})
elseif (SPHINX_VERSION_OUTPUT_VARIABLE MATCHES ".*build[ )]*(.*)")
set(_version ${CMAKE_MATCH_1})
endif()
set(SPHINX_EXECUTABLE_VERSION ${_version} CACHE INTERNAL "Version of ${SPHINX_EXECUTABLE}")
endif() endif()
set(_find_deps_options) set(_find_deps_options)
......
...@@ -191,8 +191,9 @@ macro (gmx_c_flags) ...@@ -191,8 +191,9 @@ macro (gmx_c_flags)
endif() endif()
if (GMX_COMPILER_WARNINGS) if (GMX_COMPILER_WARNINGS)
#only on Windows #only on Windows
#161: unrecognized pragma
#1786 function was declared deprecated (is issued for stdlib function such as strncpy which have a _s version) #1786 function was declared deprecated (is issued for stdlib function such as strncpy which have a _s version)
GMX_TEST_CFLAG(CFLAGS_WARN "/W3 /wd177 /wd411 /wd593 /wd981 /wd1418 /wd1419 /wd1572 /wd1599 /wd1786 /wd2259 /wd2415 /wd2547 /wd2557 /wd3280" GMXC_CFLAGS) GMX_TEST_CFLAG(CFLAGS_WARN "/W3 /wd161 /wd177 /wd411 /wd593 /wd981 /wd1418 /wd1419 /wd1572 /wd1599 /wd1786 /wd2259 /wd2415 /wd2547 /wd2557 /wd3280" GMXC_CFLAGS)
endif() endif()
GMX_TEST_CFLAG(CFLAGS_OPT "/Qip" GMXC_CFLAGS_RELEASE) GMX_TEST_CFLAG(CFLAGS_OPT "/Qip" GMXC_CFLAGS_RELEASE)
endif() endif()
...@@ -229,8 +230,9 @@ GMX_TEST_CFLAG(CFLAGS_WARN "/W3 /wd177 /wd411 /wd593 /wd981 /wd1418 /wd1419 /wd1 ...@@ -229,8 +230,9 @@ GMX_TEST_CFLAG(CFLAGS_WARN "/W3 /wd177 /wd411 /wd593 /wd981 /wd1418 /wd1419 /wd1
GMX_TEST_CXXFLAG(CXXFLAGS_PRAGMA "/wd3180" GMXC_CFLAGS) GMX_TEST_CXXFLAG(CXXFLAGS_PRAGMA "/wd3180" GMXC_CFLAGS)
endif() endif()
if (GMX_COMPILER_WARNINGS) if (GMX_COMPILER_WARNINGS)
#161: unrecognized pragma
#809: exception specification for virtual function X is incompatible with that of overridden function #809: exception specification for virtual function X is incompatible with that of overridden function
GMX_TEST_CXXFLAG(CXXFLAGS_WARN "/W3 /wd177 /wd304 /wd383 /wd411 /wd444 /wd809 /wd869 /wd981 /wd1418 /wd1572 /wd1599 /wd1786 /wd2259 /wd2547 /wd3280 /wd11074 /wd11076 /wd2282" GMXC_CXXFLAGS) GMX_TEST_CXXFLAG(CXXFLAGS_WARN "/W3 /wd161 /wd177 /wd304 /wd383 /wd411 /wd444 /wd809 /wd869 /wd981 /wd1418 /wd1572 /wd1599 /wd1786 /wd2259 /wd2547 /wd3280 /wd11074 /wd11076 /wd2282" GMXC_CXXFLAGS)
endif() endif()
GMX_TEST_CXXFLAG(CXXFLAGS_OPT "/Qip" GMXC_CXXFLAGS_RELEASE) GMX_TEST_CXXFLAG(CXXFLAGS_OPT "/Qip" GMXC_CXXFLAGS_RELEASE)
endif() endif()
...@@ -301,11 +303,12 @@ GMX_TEST_CFLAG(CFLAGS_WARN "/W3 /wd177 /wd411 /wd593 /wd981 /wd1418 /wd1419 /wd1 ...@@ -301,11 +303,12 @@ GMX_TEST_CFLAG(CFLAGS_WARN "/W3 /wd177 /wd411 /wd593 /wd981 /wd1418 /wd1419 /wd1
# unreferenced local variable (only C) # unreferenced local variable (only C)
# conversion from 'size_t' to 'int', possible loss of data # conversion from 'size_t' to 'int', possible loss of data
# conversion from 'const char*' to 'void*', different 'const' qualifiers (only C) # conversion from 'const char*' to 'void*', different 'const' qualifiers (only C)
# unknown pragma (4068)
if(NOT CMAKE_CONFIGURATION_TYPES) if(NOT CMAKE_CONFIGURATION_TYPES)
GMX_TEST_CFLAG(CFLAGS_WARN "/wd4800 /wd4355 /wd4996 /wd4305 /wd4244 /wd4101 /wd4267 /wd4090" GMXC_CFLAGS) GMX_TEST_CFLAG(CFLAGS_WARN "/wd4800 /wd4355 /wd4996 /wd4305 /wd4244 /wd4101 /wd4267 /wd4090 /wd4068" GMXC_CFLAGS)
GMX_TEST_CXXFLAG(CXXFLAGS_WARN "/wd4800 /wd4355 /wd4996 /wd4305 /wd4244 /wd4267" GMXC_CXXFLAGS) GMX_TEST_CXXFLAG(CXXFLAGS_WARN "/wd4800 /wd4355 /wd4996 /wd4305 /wd4244 /wd4267 /wd4068" GMXC_CXXFLAGS)
else() #Projects only use the C++ flags else() # MSVC projects only use the C++ flags
GMX_TEST_CXXFLAG(CXXFLAGS_WARN "/wd4800 /wd4355 /wd4996 /wd4305 /wd4244 /wd4101 /wd4267 /wd4090" GMXC_CXXFLAGS) GMX_TEST_CXXFLAG(CXXFLAGS_WARN "/wd4800 /wd4355 /wd4996 /wd4305 /wd4244 /wd4101 /wd4267 /wd4090 /wd4068" GMXC_CXXFLAGS)
endif() endif()
endif() endif()
......
...@@ -43,6 +43,7 @@ gmx_option_multichoice(GMX_USE_LMFIT ...@@ -43,6 +43,7 @@ gmx_option_multichoice(GMX_USE_LMFIT
"How to handle the lmfit dependency of GROMACS" "How to handle the lmfit dependency of GROMACS"
INTERNAL INTERNAL
INTERNAL EXTERNAL NONE) INTERNAL EXTERNAL NONE)
mark_as_advanced(GMX_USE_LMFIT)
# Make a fully functional lmfit library target that libgromacs can # Make a fully functional lmfit library target that libgromacs can
# depend on regardless of how the user directed lmfit support and/or # depend on regardless of how the user directed lmfit support and/or
......
...@@ -66,4 +66,5 @@ function(GMX_TEST_IMAGEMAGICK VARIABLE) ...@@ -66,4 +66,5 @@ function(GMX_TEST_IMAGEMAGICK VARIABLE)
endif() endif()
endif() endif()
set(${VARIABLE} ${value_} CACHE INTERNAL "Test if image conversion works") set(${VARIABLE} ${value_} CACHE INTERNAL "Test if image conversion works")
mark_as_advanced(${VARIABLE})
endfunction() endfunction()
...@@ -201,7 +201,7 @@ set(GMX_VERSION_PATCH 0) ...@@ -201,7 +201,7 @@ set(GMX_VERSION_PATCH 0)
# 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
# as after the final release is out. # as after the final release is out.
set(GMX_VERSION_SUFFIX "-beta2") set(GMX_VERSION_SUFFIX "-beta3")
# Conventionally with libtool, any ABI change must change the major # Conventionally with libtool, any ABI change must change the major
# version number, the minor version number should change if it's just # version number, the minor version number should change if it's just
...@@ -235,13 +235,13 @@ if (NOT SOURCE_IS_SOURCE_DISTRIBUTION AND ...@@ -235,13 +235,13 @@ if (NOT SOURCE_IS_SOURCE_DISTRIBUTION AND
endif() endif()
set(REGRESSIONTEST_VERSION "${GMX_VERSION_STRING}") set(REGRESSIONTEST_VERSION "${GMX_VERSION_STRING}")
set(REGRESSIONTEST_BRANCH "refs/heads/master") set(REGRESSIONTEST_BRANCH "refs/heads/release-2019")
# Run the regressiontests packaging job with the correct pakage # Run the regressiontests packaging job with the correct pakage
# version string, and the release box checked, in order to have it # version string, and the release box checked, in order to have it
# build the regressiontests tarball with all the right naming. The # build the regressiontests tarball with all the right naming. The
# naming affects the md5sum that has to go here, and if it isn't right # naming affects the md5sum that has to go here, and if it isn't right
# release workflow will report a failure. # release workflow will report a failure.
set(REGRESSIONTEST_MD5SUM "3d06d41e07f523d70ae575b9ad75c670" CACHE INTERNAL "MD5 sum of the regressiontests tarball for this GROMACS version") set(REGRESSIONTEST_MD5SUM "10279cbb59912e11959fdd3981ad9c6f" CACHE INTERNAL "MD5 sum of the regressiontests tarball for this GROMACS version")
math(EXPR GMX_VERSION_NUMERIC math(EXPR GMX_VERSION_NUMERIC
"${GMX_VERSION_MAJOR}*10000 + ${GMX_VERSION_PATCH}") "${GMX_VERSION_MAJOR}*10000 + ${GMX_VERSION_PATCH}")
......
...@@ -373,6 +373,7 @@ if (SPHINX_FOUND) ...@@ -373,6 +373,7 @@ if (SPHINX_FOUND)
release-notes/2019/major/deprecated-functionality.rst release-notes/2019/major/deprecated-functionality.rst
release-notes/2019/major/portability.rst release-notes/2019/major/portability.rst
release-notes/2019/major/miscellaneous.rst release-notes/2019/major/miscellaneous.rst
release-notes/2018/2018.5.rst
release-notes/2018/2018.4.rst release-notes/2018/2018.4.rst
release-notes/2018/2018.3.rst release-notes/2018/2018.3.rst
release-notes/2018/2018.2.rst release-notes/2018/2018.2.rst
......
...@@ -208,6 +208,18 @@ Variables affecting compilation/linking ...@@ -208,6 +208,18 @@ Variables affecting compilation/linking
subcounters which are available. subcounters which are available.
Defaults to ``OFF``. Defaults to ``OFF``.
.. cmake:: GMX_ENABLE_CCACHE
If set to ``ON``, attempts to set up the `ccache <https://ccache.samba.org>`_
caching compiler wrapper to speed up repeated builds.
The ``ccache`` executable is searched for with ``find_package()`` if CMake
is being run with a compatible build type.
If the executable is found and a compatible compiler is configured,
CMake launch wrapper scripts are set.
If enabled, the ``ccache`` executable location discovered by CMake must be
accessible during build, as well.
Defaults to ``OFF`` to minimize build system complexity.
.. cmake:: GMX_INSTALL_DATASUBDIR .. cmake:: GMX_INSTALL_DATASUBDIR
Sets the subdirectory under CMAKE_INSTALL_DATADIR where GROMACS-specific Sets the subdirectory under CMAKE_INSTALL_DATADIR where GROMACS-specific
...@@ -337,6 +349,15 @@ Variables affecting the ``all`` target ...@@ -337,6 +349,15 @@ Variables affecting the ``all`` target
Variables affecting special targets Variables affecting special targets
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. cmake:: GMXAPI
If set ``ON``, the additional ``gmxapi`` C++ library is configured and the
``gmxapi`` headers will be installed. Provides the additional build tree
targets ``gmxapi-cppdocs`` and ``gmxapi-cppdocs-dev`` when Doxygen is
available. Also exports CMake configuration files for ``gmxapi`` that allow
``find_package(gmxapi)`` to import the ``Gromacs::gmxapi`` CMake target in
client projects that search the GROMACS installation root.
.. cmake:: GMX_BUILD_MANUAL .. cmake:: GMX_BUILD_MANUAL
If set ``ON``, CMake detection for LaTeX and other prerequisites for the If set ``ON``, CMake detection for LaTeX and other prerequisites for the
...@@ -441,6 +462,12 @@ doxygen-* ...@@ -441,6 +462,12 @@ doxygen-*
turn runs as part of the Jenkins documentation job. turn runs as part of the Jenkins documentation job.
All CMake code is in :file:`docs/doxygen/`. All CMake code is in :file:`docs/doxygen/`.
See :doc:`doxygen`. See :doc:`doxygen`.
gmxapi-cppdocs
Builds API documentation for gmxapi. Useful to authors of client software.
Documentation is generated in :file:`docs/api-user` in the build directory.
gmxapi-cppdocs-dev
Extract documentation for gmxapi and GROMACS developers to
:file:`docs/api-dev`.
install-guide install-guide
Runs Sphinx to generate a plain-text INSTALL file for the source package. Runs Sphinx to generate a plain-text INSTALL file for the source package.
The files is generated at :file:`docs/install-guide/text/`, from where it The files is generated at :file:`docs/install-guide/text/`, from where it
......
...@@ -63,16 +63,6 @@ Build system ...@@ -63,16 +63,6 @@ Build system
CMake CMake
Main tool used in the build system. Main tool used in the build system.
ccache
When ``GMX_ENABLE_CCACHE`` is set, the `ccache
<https://ccache.samba.org>`_ caching compiler wrapper must be found
on the PATH, together with a supported compiler, so that a caching
compiler wrapper will be used with CMake. Not all compilers are
supported. Refer to the ``GMX_ENABLE_CCACHE`` option in
``CMakeLists.txt`` and to ``cmake/gmxManageCcache.cmake`` for
details. Please submit updates if you find that the current
configuration is too conservative.
packaging for distribution (CPack) packaging for distribution (CPack)
unit testing (CTest) unit testing (CTest)
......
...@@ -764,7 +764,7 @@ gmxapi external API ...@@ -764,7 +764,7 @@ gmxapi external API
For dynamic linking builds and on non-Windows platforms, an extra library and For dynamic linking builds and on non-Windows platforms, an extra library and
headers are installed by setting ``-DGMXAPI=ON`` (default). headers are installed by setting ``-DGMXAPI=ON`` (default).
Build targets ``gmxapi_cppdocs`` and ``gmxapi_cppdocs_dev`` produce documentation in Build targets ``gmxapi-cppdocs`` and ``gmxapi-cppdocs-dev`` produce documentation in
``docs/api-user`` and ``docs/api-dev``, respectively. ``docs/api-user`` and ``docs/api-dev``, respectively.
For more project information and use cases, For more project information and use cases,
refer to the tracked :issue:`2585`, refer to the tracked :issue:`2585`,
......
.\" Man page generated from reStructuredText. .\" Man page generated from reStructuredText.
. .
.TH "GMX-ANADOCK" "1" "Nov 06, 2018" "2019-beta2" "GROMACS" .TH "GMX-ANADOCK" "1" "Nov 22, 2018" "2019-beta3" "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" "Nov 06, 2018" "2019-beta2" "GROMACS" .TH "GMX-ANAEIG" "1" "Nov 22, 2018" "2019-beta3" "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" "Nov 06, 2018" "2019-beta2" "GROMACS" .TH "GMX-ANALYZE" "1" "Nov 22, 2018" "2019-beta3" "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" "Nov 06, 2018" "2019-beta2" "GROMACS" .TH "GMX-ANGLE" "1" "Nov 22, 2018" "2019-beta3" "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" "Nov 06, 2018" "2019-beta2" "GROMACS" .TH "GMX-AWH" "1" "Nov 22, 2018" "2019-beta3" "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" "Nov 06, 2018" "2019-beta2" "GROMACS" .TH "GMX-BAR" "1" "Nov 22, 2018" "2019-beta3" "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" "Nov 06, 2018" "2019-beta2" "GROMACS" .TH "GMX-BUNDLE" "1" "Nov 22, 2018" "2019-beta3" "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" "Nov 06, 2018" "2019-beta2" "GROMACS" .TH "GMX-CHECK" "1" "Nov 22, 2018" "2019-beta3" "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" "Nov 06, 2018" "2019-beta2" "GROMACS" .TH "GMX-CHI" "1" "Nov 22, 2018" "2019-beta3" "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" "Nov 06, 2018" "2019-beta2" "GROMACS" .TH "GMX-CLUSTER" "1" "Nov 22, 2018" "2019-beta3" "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" "Nov 06, 2018" "2019-beta2" "GROMACS" .TH "GMX-CLUSTSIZE" "1" "Nov 22, 2018" "2019-beta3" "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" "Nov 06, 2018" "2019-beta2" "GROMACS" .TH "GMX-CONFRMS" "1" "Nov 22, 2018" "2019-beta3" "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" "Nov 06, 2018" "2019-beta2" "GROMACS" .TH "GMX-CONVERT-TPR" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME .SH NAME
gmx-convert-tpr \- Make a modifed run-input file gmx-convert-tpr \- Make a modifed run-input file
. .
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.TH "GMX-COVAR" "1" "Nov 06, 2018" "2019-beta2" "GROMACS" .TH "GMX-COVAR" "1" "Nov 22, 2018" "2019-beta3" "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" "Nov 06, 2018" "2019-beta2" "GROMACS" .TH "GMX-CURRENT" "1" "Nov 22, 2018" "2019-beta3" "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" "Nov 06, 2018" "2019-beta2" "GROMACS" .TH "GMX-DENSITY" "1" "Nov 22, 2018" "2019-beta3" "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" "Nov 06, 2018" "2019-beta2" "GROMACS" .TH "GMX-DENSMAP" "1" "Nov 22, 2018" "2019-beta3" "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" "Nov 06, 2018" "2019-beta2" "GROMACS" .TH "GMX-DENSORDER" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME .SH NAME
gmx-densorder \- Calculate surface fluctuations gmx-densorder \- Calculate surface fluctuations
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.TH "GMX-DIELECTRIC" "1" "Nov 06, 2018" "2019-beta2" "GROMACS" .TH "GMX-DIELECTRIC" "1" "Nov 22, 2018" "2019-beta3" "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" "Nov 06, 2018" "2019-beta2" "GROMACS" .TH "GMX-DIPOLES" "1" "Nov 22, 2018" "2019-beta3" "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" "Nov 06, 2018" "2019-beta2" "GROMACS" .TH "GMX-DISRE" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME .SH NAME
gmx-disre \- Analyze distance restraints gmx-disre \- Analyze distance restraints
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.TH "GMX-DISTANCE" "1" "Nov 06, 2018" "2019-beta2" "GROMACS" .TH "GMX-DISTANCE" "1" "Nov 22, 2018" "2019-beta3" "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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.TH "GMX-DO_DSSP" "1" "Nov 06, 2018" "2019-beta2" "GROMACS" .TH "GMX-DO_DSSP" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME .SH NAME
gmx-do_dssp \- Assign secondary structure and calculate solvent accessible surface area gmx-do_dssp \- Assign secondary structure and calculate solvent accessible surface area
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.TH "GMX-DOS" "1" "Nov 06, 2018" "2019-beta2" "GROMACS" .TH "GMX-DOS" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME .SH NAME
gmx-dos \- Analyze density of states and properties based on that gmx-dos \- Analyze density of states and properties based on that
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.TH "GMX-DUMP" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"