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

New upstream version 2019~beta3

parent c8d5e6b8
......@@ -5,7 +5,7 @@ Installation guide
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.
......@@ -28,8 +28,8 @@ Quick and dirty installation
Or, as a sequence of commands to execute:
tar xfz gromacs-2019-beta2.tar.gz
cd gromacs-2019-beta2
tar xfz gromacs-2019-beta3.tar.gz
cd gromacs-2019-beta3
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
......@@ -166,7 +166,7 @@ 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-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.
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
code you want to build. For example, download the source tarball and
use
tar xfz gromacs-2019-beta2.tgz
cd gromacs-2019-beta2
tar xfz gromacs-2019-beta3.tgz
cd gromacs-2019-beta3
mkdir build-gromacs
cd build-gromacs
cmake ..
......@@ -799,7 +799,7 @@ gmxapi external API
For dynamic linking builds and on non-Windows platforms, an extra
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
more project information and use cases, refer to the tracked Issue
2585, associated GitHub gmxapi projects, or DOI
......@@ -1022,7 +1022,7 @@ 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-2019-beta2.tar.gz
http://gerrit.gromacs.org/download/regressiontests-2019-beta3.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
......
......@@ -11,7 +11,7 @@
# Test on ARM v7
# 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 ARM_NEON_ASIMD SIMD
......@@ -67,7 +67,7 @@ icc-18 msvc-2017 fftpack simd=avx2_256 release
#gcc-7 armhpc-18.2 openmp simd=ARM_NEON_ASIMD release
# 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
# Add SIMD + OpenMP + CUDA asan build
......
#
# 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,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
......@@ -85,6 +85,7 @@ if(HWLOC_INCLUDE_DIRS)
# If we are not cross-compiling we try to use the hwloc-info program
if(NOT CMAKE_CROSSCOMPILING)
find_program(HWLOC_INFO "hwloc-info")
mark_as_advanced(HWLOC_INFO)
if(HWLOC_INFO)
execute_process(COMMAND ${HWLOC_INFO} "--version"
......
......@@ -50,8 +50,19 @@ if (SPHINX_EXECUTABLE AND NOT DEFINED SPHINX_EXECUTABLE_VERSION)
ERROR_QUIET
OUTPUT_STRIP_TRAILING_WHITESPACE
)
string(REGEX REPLACE ".*build[ )]*" "" SPHINX_EXECUTABLE_VERSION "${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()
set(_find_deps_options)
......
......@@ -191,8 +191,9 @@ macro (gmx_c_flags)
endif()
if (GMX_COMPILER_WARNINGS)
#only on Windows
#161: unrecognized pragma
#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()
GMX_TEST_CFLAG(CFLAGS_OPT "/Qip" GMXC_CFLAGS_RELEASE)
endif()
......@@ -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)
endif()
if (GMX_COMPILER_WARNINGS)
#161: unrecognized pragma
#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()
GMX_TEST_CXXFLAG(CXXFLAGS_OPT "/Qip" GMXC_CXXFLAGS_RELEASE)
endif()
......@@ -301,11 +303,12 @@ GMX_TEST_CFLAG(CFLAGS_WARN "/W3 /wd177 /wd411 /wd593 /wd981 /wd1418 /wd1419 /wd1
# unreferenced local variable (only C)
# conversion from 'size_t' to 'int', possible loss of data
# conversion from 'const char*' to 'void*', different 'const' qualifiers (only C)
# unknown pragma (4068)
if(NOT CMAKE_CONFIGURATION_TYPES)
GMX_TEST_CFLAG(CFLAGS_WARN "/wd4800 /wd4355 /wd4996 /wd4305 /wd4244 /wd4101 /wd4267 /wd4090" GMXC_CFLAGS)
GMX_TEST_CXXFLAG(CXXFLAGS_WARN "/wd4800 /wd4355 /wd4996 /wd4305 /wd4244 /wd4267" GMXC_CXXFLAGS)
else() #Projects only use the C++ flags
GMX_TEST_CXXFLAG(CXXFLAGS_WARN "/wd4800 /wd4355 /wd4996 /wd4305 /wd4244 /wd4101 /wd4267 /wd4090" GMXC_CXXFLAGS)
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 /wd4068" GMXC_CXXFLAGS)
else() # MSVC projects only use the C++ flags
GMX_TEST_CXXFLAG(CXXFLAGS_WARN "/wd4800 /wd4355 /wd4996 /wd4305 /wd4244 /wd4101 /wd4267 /wd4090 /wd4068" GMXC_CXXFLAGS)
endif()
endif()
......
......@@ -43,6 +43,7 @@ gmx_option_multichoice(GMX_USE_LMFIT
"How to handle the lmfit dependency of GROMACS"
INTERNAL
INTERNAL EXTERNAL NONE)
mark_as_advanced(GMX_USE_LMFIT)
# Make a fully functional lmfit library target that libgromacs can
# depend on regardless of how the user directed lmfit support and/or
......
......@@ -66,4 +66,5 @@ function(GMX_TEST_IMAGEMAGICK VARIABLE)
endif()
endif()
set(${VARIABLE} ${value_} CACHE INTERNAL "Test if image conversion works")
mark_as_advanced(${VARIABLE})
endfunction()
......@@ -201,7 +201,7 @@ set(GMX_VERSION_PATCH 0)
# candidates, where it signifies the most recent such release from
# this branch; it will be empty before the first such release, as well
# 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
# version number, the minor version number should change if it's just
......@@ -235,13 +235,13 @@ if (NOT SOURCE_IS_SOURCE_DISTRIBUTION AND
endif()
set(REGRESSIONTEST_VERSION "${GMX_VERSION_STRING}")
set(REGRESSIONTEST_BRANCH "refs/heads/master")
set(REGRESSIONTEST_BRANCH "refs/heads/release-2019")
# Run the regressiontests packaging job with the correct pakage
# version string, and the release box checked, in order to have it
# build the regressiontests tarball with all the right naming. The
# naming affects the md5sum that has to go here, and if it isn't right
# release workflow will report a failure.
set(REGRESSIONTEST_MD5SUM "3d06d41e07f523d70ae575b9ad75c670" CACHE INTERNAL "MD5 sum of the regressiontests tarball for this GROMACS version")
set(REGRESSIONTEST_MD5SUM "10279cbb59912e11959fdd3981ad9c6f" CACHE INTERNAL "MD5 sum of the regressiontests tarball for this GROMACS version")
math(EXPR GMX_VERSION_NUMERIC
"${GMX_VERSION_MAJOR}*10000 + ${GMX_VERSION_PATCH}")
......
......@@ -373,6 +373,7 @@ if (SPHINX_FOUND)
release-notes/2019/major/deprecated-functionality.rst
release-notes/2019/major/portability.rst
release-notes/2019/major/miscellaneous.rst
release-notes/2018/2018.5.rst
release-notes/2018/2018.4.rst
release-notes/2018/2018.3.rst
release-notes/2018/2018.2.rst
......
......@@ -208,6 +208,18 @@ Variables affecting compilation/linking
subcounters which are available.
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
Sets the subdirectory under CMAKE_INSTALL_DATADIR where GROMACS-specific
......@@ -337,6 +349,15 @@ Variables affecting the ``all`` target
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
If set ``ON``, CMake detection for LaTeX and other prerequisites for the
......@@ -441,6 +462,12 @@ doxygen-*
turn runs as part of the Jenkins documentation job.
All CMake code is in :file:`docs/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
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
......
......@@ -63,16 +63,6 @@ Build system
CMake
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)
unit testing (CTest)
......
......@@ -764,7 +764,7 @@ gmxapi external API
For dynamic linking builds and on non-Windows platforms, an extra library and
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.
For more project information and use cases,
refer to the tracked :issue:`2585`,
......
.\" 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
gmx-anadock \- Cluster structures from Autodock runs
.
......
.\" 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
gmx-anaeig \- Analyze eigenvectors/normal modes
.
......
.\" 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
gmx-analyze \- Analyze data sets
.
......
.\" 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
gmx-angle \- Calculate distributions and correlations for angles and dihedrals
.
......
.\" 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
gmx-awh \- Extract data from an accelerated weight histogram (AWH) run
.
......
.\" 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
gmx-bar \- Calculate free energy difference estimates through Bennett's acceptance ratio
.
......
.\" 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
gmx-bundle \- Analyze bundles of axes, e.g., helices
.
......
.\" 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
gmx-check \- Check and compare files
.
......
.\" 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
gmx-chi \- Calculate everything you want to know about chi and other dihedrals
.
......
.\" 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
gmx-cluster \- Cluster structures
.
......
.\" 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
gmx-clustsize \- Calculate size distributions of atomic clusters
.
......
.\" 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
gmx-confrms \- Fit two structures and calculates the RMSD
.
......
.\" 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
gmx-convert-tpr \- Make a modifed run-input file
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-COVAR" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-COVAR" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-covar \- Calculate and diagonalize the covariance matrix
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CURRENT" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-CURRENT" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-current \- Calculate dielectric constants and current autocorrelation function
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DENSITY" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-DENSITY" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-density \- Calculate the density of the system
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DENSMAP" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-DENSMAP" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-densmap \- Calculate 2D planar or axial-radial density maps
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DENSORDER" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-DENSORDER" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-densorder \- Calculate surface fluctuations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DIELECTRIC" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-DIELECTRIC" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-dielectric \- Calculate frequency dependent dielectric constants
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DIPOLES" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-DIPOLES" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-dipoles \- Compute the total dipole plus fluctuations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DISRE" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-DISRE" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-disre \- Analyze distance restraints
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DISTANCE" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-DISTANCE" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-distance \- Calculate distances between pairs of positions
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DO_DSSP" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-DO_DSSP" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-do_dssp \- Assign secondary structure and calculate solvent accessible surface area
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DOS" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-DOS" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-dos \- Analyze density of states and properties based on that
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DUMP" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-DUMP" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-dump \- Make binary files human readable
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DYECOUPL" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-DYECOUPL" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-dyecoupl \- Extract dye dynamics from trajectories
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DYNDOM" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-DYNDOM" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-dyndom \- Interpolate and extrapolate structure rotations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-EDITCONF" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-EDITCONF" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-editconf \- Convert and manipulates structure files
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ENECONV" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-ENECONV" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-eneconv \- Convert energy files
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ENEMAT" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-ENEMAT" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-enemat \- Extract an energy matrix from an energy file
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ENERGY" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-ENERGY" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-energy \- Writes energies to xvg files and display averages
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-FILTER" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-FILTER" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-filter \- Frequency filter trajectories, useful for making smooth movies
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-FREEVOLUME" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-FREEVOLUME" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-freevolume \- Calculate free volume
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-GANGLE" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-GANGLE" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-gangle \- Calculate angles
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-GENCONF" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-GENCONF" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-genconf \- Multiply a conformation in 'random' orientations
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.TH "GMX-GENION" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-GENION" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-genion \- Generate monoatomic ions on energetically favorable positions
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.TH "GMX-GENRESTR" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-GENRESTR" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-genrestr \- Generate position restraints or distance restraints for index groups
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.TH "GMX-GROMPP" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-GROMPP" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-grompp \- Make a run input file
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.TH "GMX-GYRATE" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-GYRATE" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-gyrate \- Calculate the radius of gyration
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.TH "GMX-H2ORDER" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-H2ORDER" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-h2order \- Compute the orientation of water molecules
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.TH "GMX-HBOND" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-HBOND" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-hbond \- Compute and analyze hydrogen bonds
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.TH "GMX-HELIX" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-HELIX" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-helix \- Calculate basic properties of alpha helices
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.TH "GMX-HELIXORIENT" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-HELIXORIENT" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-helixorient \- Calculate local pitch/bending/rotation/orientation inside helices
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.TH "GMX-HELP" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-HELP" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-help \- Print help information
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.TH "GMX-HYDORDER" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-HYDORDER" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-hydorder \- Compute tetrahedrality parameters around a given atom
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.TH "GMX-INSERT-MOLECULES" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-INSERT-MOLECULES" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-insert-molecules \- Insert molecules into existing vacancies
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.TH "GMX-LIE" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-LIE" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-lie \- Estimate free energy from linear combinations
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.TH "GMX-MAKE_EDI" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-MAKE_EDI" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-make_edi \- Generate input files for essential dynamics sampling
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.TH "GMX-MAKE_NDX" "1" "Nov 06, 2018" "2019-beta2" "GROMACS"
.TH "GMX-MAKE_NDX" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.SH NAME
gmx-make_ndx \- Make index files