Commit 8f966be4 authored by Nicholas Breen's avatar Nicholas Breen

New upstream version 2018.2

parent 1d960618
#
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
# Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018, 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.
......@@ -808,36 +808,28 @@ else()
set(GMX_SHARED_LINKER_FLAGS ${GMX_SHARED_LINKER_FLAGS} ${OpenMP_SHARED_LINKER_FLAGS})
endif()
########################################################################
# Specify install locations
########################################################################
# Use GNUInstallDirs to set paths on multiarch systems.
include(GNUInstallDirs)
# Customization for the installation tree paths.
set(GMX_LIB_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR} CACHE STRING
"Library installation directory (default: ${CMAKE_INSTALL_LIBDIR})")
set(GMX_DATA_INSTALL_DIR gromacs CACHE STRING
"Data installation directory under share/ (default: gromacs)")
mark_as_advanced(GMX_LIB_INSTALL_DIR GMX_DATA_INSTALL_DIR)
# These variables are used internally to provide a central location for
# customizing the install locations.
set(LIB_INSTALL_DIR ${GMX_LIB_INSTALL_DIR})
set(BIN_INSTALL_DIR bin)
# This variable also gets written into config.h for use in finding the data
# directories.
set(DATA_INSTALL_DIR share/${GMX_DATA_INSTALL_DIR})
set(MAN_INSTALL_DIR share/man)
set(GMX_INSTALL_DATASUBDIR "gromacs" CACHE STRING "Subdirectory for GROMACS data under CMAKE_INSTALL_DATADIR")
mark_as_advanced(GMX_INSTALL_DATASUBDIR)
# Internal convenience so we do not have to join two path segments in the code
set(GMX_INSTALL_GMXDATADIR ${CMAKE_INSTALL_DATADIR}/${GMX_INSTALL_DATASUBDIR})
# If the nesting level wrt. the installation root is changed,
# gromacs-config.cmake.cmakein needs to be adapted.
set(CMAKE_INSTALL_DIR share/cmake)
set(GMX_INSTALL_CMAKEDIR ${CMAKE_INSTALL_DATAROOTDIR}/cmake)
# TODO: Make GMXRC adapt if this is changed
set(PKGCONFIG_INSTALL_DIR ${LIB_INSTALL_DIR}/pkgconfig)
set(OCL_INSTALL_DIR ${DATA_INSTALL_DIR}/opencl)
set(INCL_INSTALL_DIR include)
set(GMX_INSTALL_PKGCONFIGDIR ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
set(GMX_INSTALL_OCLDIR ${GMX_INSTALL_GMXDATADIR}/opencl)
list(APPEND INSTALLED_HEADER_INCLUDE_DIRS ${INCL_INSTALL_DIR})
list(APPEND INSTALLED_HEADER_INCLUDE_DIRS ${CMAKE_INSTALL_INCLUDEDIR})
# Binary and library suffix options
include(gmxManageSuffixes)
......@@ -855,7 +847,7 @@ else()
# install to lib/, then the installation RPATH works also in the build
# tree. This makes installation slightly faster (no need to rewrite the
# RPATHs), and makes the binaries in the build tree relocatable.
if(GMX_LIB_INSTALL_DIR STREQUAL "lib")
if(CMAKE_INSTALL_LIBDIR STREQUAL "lib")
set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
if(POLICY CMP0068)
cmake_policy(SET CMP0068 NEW) # From CMake-3.9
......@@ -865,10 +857,10 @@ else()
# Set the RPATH as relative to the executable location to make the
# binaries relocatable.
if(CMAKE_SYSTEM_NAME STREQUAL "Darwin") #Assume OS X >=10.5
set(CMAKE_INSTALL_RPATH "@executable_path/../${GMX_LIB_INSTALL_DIR}")
set(CMAKE_INSTALL_RPATH "@executable_path/../${CMAKE_INSTALL_LIBDIR}")
set(CMAKE_INSTALL_NAME_DIR ${CMAKE_INSTALL_RPATH})
else()
set(CMAKE_INSTALL_RPATH "\$ORIGIN/../${GMX_LIB_INSTALL_DIR}")
set(CMAKE_INSTALL_RPATH "\$ORIGIN/../${CMAKE_INSTALL_LIBDIR}")
endif()
set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
set(CMAKE_MACOSX_RPATH 1)
......@@ -876,7 +868,7 @@ endif()
#COPYING file: Only necessary for binary distributions.
#Simpler to always install.
install(FILES COPYING DESTINATION ${DATA_INSTALL_DIR} COMPONENT data)
install(FILES COPYING DESTINATION ${GMX_INSTALL_GMXDATADIR} COMPONENT data)
if (GMX_BUILD_FOR_COVERAGE)
# Code heavy with asserts makes conditional coverage close to useless metric,
......
......@@ -5,7 +5,7 @@ Installation guide
Introduction to building GROMACS
================================
These instructions pertain to building GROMACS 2018.1. You might also
These instructions pertain to building GROMACS 2018.2. 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-2018.1.tar.gz
cd gromacs-2018.1
tar xfz gromacs-2018.2.tar.gz
cd gromacs-2018.2
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-2018.1. We recommend to use the gcc compiler
architectures for GROMACS-2018.2. 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-2018.1.tgz
cd gromacs-2018.1
tar xfz gromacs-2018.2.tgz
cd gromacs-2018.2
mkdir build-gromacs
cd build-gromacs
cmake ..
......@@ -875,7 +875,8 @@ renamed by editing the installation paths in the main CMakeLists.txt.
"bin/"
The standard location for executables and some scripts. Some of the
scripts hardcode the absolute installation prefix, which needs to
be changed if the scripts are relocated.
be changed if the scripts are relocated. The name of the directory
can be changed using "CMAKE_INSTALL_BINDIR" CMake variable.
"include/gromacs/"
The standard location for installed headers.
......@@ -883,7 +884,7 @@ renamed by editing the installation paths in the main CMakeLists.txt.
"lib/"
The standard location for libraries. The default depends on the
system, and is determined by CMake. The name of the directory can
be changed using "GMX_LIB_INSTALL_DIR" CMake variable.
be changed using "CMAKE_INSTALL_LIBDIR" CMake variable.
"lib/pkgconfig/"
Information about the installed "libgromacs" library for "pkg-
......@@ -895,9 +896,10 @@ renamed by editing the installation paths in the main CMakeLists.txt.
CMake package configuration files are installed here.
"share/gromacs/"
Various data files and some documentation go here. The "gromacs"
part can be changed using "GMX_DATA_INSTALL_DIR". Using this CMake
variable is the preferred way of changing the installation path for
Various data files and some documentation go here. The first part
can be changed using "CMAKE_INSTALL_DATADIR", and the second by
using "GMX_INSTALL_DATASUBDIR" Using these CMake variables is the
preferred way of changing the installation path for
"share/gromacs/top/", since the path to this directory is built
into "libgromacs" as well as some scripts, both as a relative and
as an absolute path (the latter as a fallback if everything else
......@@ -992,7 +994,7 @@ 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-2018.1.tar.gz
http://gerrit.gromacs.org/download/regressiontests-2018.2.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
......
......@@ -49,13 +49,13 @@ To help us fund development, we humbly ask that you cite the GROMACS papers:
* GROMACS: A message-passing parallel molecular dynamics implementation
H.J.C. Berendsen, D. van der Spoel and R. van Drunen
Comp. Phys. Comm. 91, 43-56 (1995)
DOI: 10.1016/0010-4655(95)00042-E
DOI: https://doi.org/10.1016/0010-4655(95)00042-E
* GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
molecular simulation
B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
J. Chem. Theory Comput. 4 (2008) pp. 435-447
DOI: 10.1021/ct700301q
DOI: https://doi.org/10.1021/ct700301q
* GROMACS 4.5: a high-throughput and highly parallel open source
molecular simulation toolkit
......@@ -63,14 +63,19 @@ To help us fund development, we humbly ask that you cite the GROMACS papers:
Rossen Apostolov, Michael R. Shirts, Jeremy C. Smith, Peter M. Kasson,
David van der Spoel, Berk Hess, Erik Lindahl.
Bioinformatics 29 (2013) pp. 845-54
DOI: 10.1093/bioinformatics/btt055
DOI: https://doi.org/10.1093/bioinformatics/btt055
* Tackling Exascale Software Challenges in Molecular Dynamics Simulations
with GROMACS
Szilárd Páll, Mark J. Abraham, Carsten Kutzner, Berk Hess, Erik Lindahl
In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale,
8759 (2015) pp. 3–27
DOI: 10.1007/978-3-319-15976-8_1
Lecture Notes for Computer Science, 8759 (2015) pp. 3–27
DOI: https://doi.org/10.1007/978-3-319-15976-8_1
* GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E. Lindahl,
SoftwareX, 1, (2015), 19-25
DOI: https://doi.org/10.1016/j.softx.2015.06.001
There are a lot of cool features we'd like to include in future versions,
but our resources are limited. All kinds of donations are welcome, both in
......
#!/usr/bin/env python2
#!/usr/bin/env python
#
# This file is part of the GROMACS molecular simulation package.
#
......
......@@ -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 1)
set(GMX_VERSION_PATCH 2)
# 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 1)
set(LIBRARY_SOVERSION_MINOR 2)
set(LIBRARY_VERSION ${LIBRARY_SOVERSION_MAJOR}.${LIBRARY_SOVERSION_MINOR}.0)
#####################################################################
......@@ -226,7 +226,12 @@ endif()
set(REGRESSIONTEST_VERSION "${GMX_VERSION_STRING}")
set(REGRESSIONTEST_BRANCH "refs/heads/release-2018")
set(REGRESSIONTEST_MD5SUM "1a94916e2cf90e34fddb3514a65e0154" CACHE INTERNAL "MD5 sum of the regressiontests tarball")
# Run the regressiontests packaging job with the correct pakage
# version string, and the release box checked, in order to have it
# build the regressiontests tarball with all the right naming. The
# naming affects the md5sum that has to go here, and if it isn't right
# release workflow will report a failure.
set(REGRESSIONTEST_MD5SUM "135149af467a37714a92bc29801cafda" CACHE INTERNAL "MD5 sum of the regressiontests tarball for this GROMACS version")
math(EXPR GMX_VERSION_NUMERIC
"${GMX_VERSION_MAJOR}*10000 + ${GMX_VERSION_PATCH}")
......
......@@ -125,6 +125,7 @@ if (SPHINX_FOUND)
fragments/doxygen-links.rst
install-guide/index.rst
release-notes/index.rst
release-notes/2018/2018.2.rst
release-notes/2018/2018.1.rst
release-notes/2018/major/highlights.rst
release-notes/2018/major/features.rst
......@@ -304,7 +305,7 @@ if (MAN_PAGE_DIR)
# Trailing slash on directory is significant for
# install(DIRECTORY). See CMake docs.
install(DIRECTORY ${MAN_PAGE_DIR}/
DESTINATION ${MAN_INSTALL_DIR}/man1
DESTINATION ${CMAKE_INSTALL_MANDIR}/man1
COMPONENT man OPTIONAL
FILES_MATCHING PATTERN "*.1")
endif()
......
......@@ -208,11 +208,12 @@ Variables affecting compilation/linking
subcounters which are available.
Defaults to ``OFF``.
.. cmake:: GMX_DATA_INSTALL_DIR
.. cmake:: GMX_INSTALL_DATASUBDIR
Sets the directory under :file:`share/` where data files are installed.
The default is ``gromacs``, which puts the files under
file:`share/gromacs/`.
Sets the subdirectory under CMAKE_INSTALL_DATADIR where GROMACS-specific
read-only architecture-independent data files are installed. The default
is ``gromacs``, which means the files will go under ``share/gromacs``.
To alter the ``share`` part, change CMAKE_INSTALL_DATADIR.
See :doc:`relocatable-binaries` for how this influences the build.
.. cmake:: GMX_DOUBLE
......@@ -265,7 +266,7 @@ Variables affecting compilation/linking
Pass additional CUDA-only compiler flags to clang using this variable.
.. cmake:: GMX_LIB_INSTALL_DIR
.. cmake:: CMAKE_INSTALL_LIBDIR
Sets the installation directory for libraries (default is determined by
standard CMake package ``GNUInstallDirs``).
......
......@@ -113,10 +113,10 @@ implementation, which works like this:
contains :file:`share/{gromacs}/top/gurgle.dat`, this directory is returned
as the installation prefix. The file name ``gurgle.dat`` and the location
are considered unique enough to ensure that the correct directory has been
found. The installation directory for the data files can be customized
during CMake configuration by setting ``GMX_DATA_INSTALL_DIR``, which
affects the *gromacs* part in the above path (both in the installation
structure and in this search logic).
found. The installation directory for read-only architecture-independent
data files can be customized during CMake configuration by setting
``CMAKE_INSTALL_DATADIR``, and the subdirectory under this that hosts the
GROMACS-specific data is set by ``GMX_INSTALL_DATASUBDIR``.
Note that this search does not resolve symbolic links or normalize the input
path beforehand: if there are ``..`` components *and* symbolic links in the
......
......@@ -821,12 +821,14 @@ CMakeLists.txt.
The standard location for executables and some scripts.
Some of the scripts hardcode the absolute installation prefix, which needs
to be changed if the scripts are relocated.
The name of the directory can be changed using ``CMAKE_INSTALL_BINDIR`` CMake
variable.
``include/gromacs/``
The standard location for installed headers.
``lib/``
The standard location for libraries. The default depends on the system, and
is determined by CMake.
The name of the directory can be changed using ``GMX_LIB_INSTALL_DIR`` CMake
The name of the directory can be changed using ``CMAKE_INSTALL_LIBDIR`` CMake
variable.
``lib/pkgconfig/``
Information about the installed ``libgromacs`` library for ``pkg-config`` is
......@@ -836,9 +838,10 @@ CMakeLists.txt.
``share/cmake/``
CMake package configuration files are installed here.
``share/gromacs/``
Various data files and some documentation go here.
The ``gromacs`` part can be changed using ``GMX_DATA_INSTALL_DIR``. Using this
CMake variable is the preferred way of changing the installation path for
Various data files and some documentation go here. The first part can
be changed using ``CMAKE_INSTALL_DATADIR``, and the second by using
``GMX_INSTALL_DATASUBDIR`` Using these CMake variables is the preferred
way of changing the installation path for
``share/gromacs/top/``, since the path to this directory is built into
``libgromacs`` as well as some scripts, both as a relative and as an absolute
path (the latter as a fallback if everything else fails).
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANADOCK" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-ANADOCK" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-anadock \- Cluster structures from Autodock runs
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANAEIG" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-ANAEIG" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-anaeig \- Analyze eigenvectors/normal modes
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANALYZE" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-ANALYZE" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-analyze \- Analyze data sets
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANGLE" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-ANGLE" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-angle \- Calculate distributions and correlations for angles and dihedrals
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-AWH" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-AWH" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-awh \- Extract data from an accelerated weight histogram (AWH) run
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-BAR" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-BAR" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-bar \- Calculate free energy difference estimates through Bennett's acceptance ratio
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-BUNDLE" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-BUNDLE" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-bundle \- Analyze bundles of axes, e.g., helices
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CHECK" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-CHECK" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-check \- Check and compare files
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CHI" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-CHI" "1" "Jun 14, 2018" "2018.2" "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" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-CLUSTER" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-cluster \- Cluster structures
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CLUSTSIZE" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-CLUSTSIZE" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-clustsize \- Calculate size distributions of atomic clusters
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CONFRMS" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-CONFRMS" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-confrms \- Fit two structures and calculates the RMSD
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CONVERT-TPR" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-CONVERT-TPR" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-convert-tpr \- Make a modifed run-input file
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-COVAR" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-COVAR" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-covar \- Calculate and diagonalize the covariance matrix
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CURRENT" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-CURRENT" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-current \- Calculate dielectric constants and current autocorrelation function
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DENSITY" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-DENSITY" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-density \- Calculate the density of the system
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DENSMAP" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-DENSMAP" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-densmap \- Calculate 2D planar or axial-radial density maps
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DENSORDER" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-DENSORDER" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-densorder \- Calculate surface fluctuations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DIELECTRIC" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-DIELECTRIC" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-dielectric \- Calculate frequency dependent dielectric constants
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DIPOLES" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-DIPOLES" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-dipoles \- Compute the total dipole plus fluctuations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DISRE" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-DISRE" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-disre \- Analyze distance restraints
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DISTANCE" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-DISTANCE" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-distance \- Calculate distances between pairs of positions
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DO_DSSP" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-DO_DSSP" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-do_dssp \- Assign secondary structure and calculate solvent accessible surface area
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DOS" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-DOS" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-dos \- Analyze density of states and properties based on that
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DUMP" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-DUMP" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-dump \- Make binary files human readable
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DYECOUPL" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-DYECOUPL" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-dyecoupl \- Extract dye dynamics from trajectories
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DYNDOM" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-DYNDOM" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-dyndom \- Interpolate and extrapolate structure rotations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-EDITCONF" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-EDITCONF" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-editconf \- Convert and manipulates structure files
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ENECONV" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-ENECONV" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-eneconv \- Convert energy files
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ENEMAT" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-ENEMAT" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-enemat \- Extract an energy matrix from an energy file
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-ENERGY" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-ENERGY" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-energy \- Writes energies to xvg files and display averages
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.TH "GMX-FILTER" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-FILTER" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-filter \- Frequency filter trajectories, useful for making smooth movies
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.TH "GMX-FREEVOLUME" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-FREEVOLUME" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-freevolume \- Calculate free volume
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.TH "GMX-GANGLE" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-GANGLE" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-gangle \- Calculate angles
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.TH "GMX-GENCONF" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-GENCONF" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-genconf \- Multiply a conformation in 'random' orientations
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.TH "GMX-GENION" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-GENION" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-genion \- Generate monoatomic ions on energetically favorable positions
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.TH "GMX-GENRESTR" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-GENRESTR" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-genrestr \- Generate position restraints or distance restraints for index groups
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.TH "GMX-GROMPP" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-GROMPP" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-grompp \- Make a run input file
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.TH "GMX-GYRATE" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-GYRATE" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-gyrate \- Calculate the radius of gyration
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.TH "GMX-H2ORDER" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-H2ORDER" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-h2order \- Compute the orientation of water molecules
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.TH "GMX-HBOND" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-HBOND" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-hbond \- Compute and analyze hydrogen bonds
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.TH "GMX-HELIX" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-HELIX" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-helix \- Calculate basic properties of alpha helices
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.TH "GMX-HELIXORIENT" "1" "Mar 21, 2018" "2018.1" "GROMACS"
.TH "GMX-HELIXORIENT" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.SH NAME
gmx-helixorient \- Calculate local pitch/bending/rotation/orientation inside helices
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