...
 
Commits (4)
......@@ -5,7 +5,7 @@ Installation guide
Introduction to building GROMACS
================================
These instructions pertain to building GROMACS 2019. You might also
These instructions pertain to building GROMACS 2019.1. 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-2019.tar.gz
cd gromacs-2019
tar xfz gromacs-2019.1.tar.gz
cd gromacs-2019.1
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 version 16.1 does not compile on
POWER architectures for GROMACS-2019. We recommend to use the gcc
POWER architectures for GROMACS-2019.1. 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
......@@ -231,16 +231,18 @@ code on the CPU. It is most reliable to use the same C++ compiler
version for GROMACS code as used as the host compiler for nvcc.
To make it possible to use other accelerators, GROMACS also includes
OpenCL support. The minimum OpenCL version required is 1.2. The
current OpenCL implementation is recommended for use with GCN-based
AMD GPUs, and on Linux we recommend the ROCm runtime. Intel integrated
GPUs are supported with the Neo drivers. OpenCL is also supported with
NVIDIA GPUs, but using the latest NVIDIA driver (which includes the
NVIDIA OpenCL runtime) is recommended. Also note that there are
performance limitations (inherent to the NVIDIA OpenCL runtime). It is
not possible to configure both CUDA and OpenCL support in the same
build of GROMACS, nor to support both Intel and other vendors’ GPUs
with OpenCL.
OpenCL support. The minimum OpenCL version required is 1.2 and only
64-bit implementations are supported. The current OpenCL
implementation is recommended for use with GCN-based AMD GPUs, and on
Linux we recommend the ROCm runtime. Intel integrated GPUs are
supported with the Neo drivers. OpenCL is also supported with NVIDIA
GPUs, but using the latest NVIDIA driver (which includes the NVIDIA
OpenCL runtime) is recommended. Also note that there are performance
limitations (inherent to the NVIDIA OpenCL runtime). It is not
possible to configure both CUDA and OpenCL support in the same build
of GROMACS, nor to support both Intel and other vendors’ GPUs with
OpenCL. A 64-bit implementation of OpenCL is required and therefore
OpenCL is only supported on 64-bit platforms.
MPI support
......@@ -437,8 +439,8 @@ 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.tgz
cd gromacs-2019
tar xfz gromacs-2019.1.tgz
cd gromacs-2019.1
mkdir build-gromacs
cd build-gromacs
cmake ..
......@@ -1041,10 +1043,11 @@ 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-2019.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-2019.1.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
......
#
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
# Copyright (c) 2015,2016,2017,2019, 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.
......@@ -34,7 +34,7 @@
import os.path
build_options = ['gcc-6', 'gcov-6']
build_options = ['gcc-7', 'gcov-7']
extra_projects = [Project.REGRESSIONTESTS]
def do_build(context):
......
#
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by
# Copyright (c) 2015,2016,2017,2018,2019, 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.
......@@ -35,6 +35,7 @@
import os
import re
build_options = ['doxygen-1.8.5']
build_out_of_source = True
extra_options = {
......@@ -57,9 +58,8 @@ def do_build(context):
cmake_opts['GMX_BUILD_TARBALL'] = 'ON'
elif context.job_type == JobType.GERRIT:
cmake_opts['GMX_COMPACT_DOXYGEN'] = 'ON'
cmake_opts.update(context.get_doc_cmake_options(
doxygen_version='1.8.5', sphinx_version='1.6.1'))
context.run_cmake(cmake_opts);
cmake_opts['DOXYGEN_EXECUTABLE'] = context.env.doxygen_command
context.run_cmake(cmake_opts)
# we keep the individual build targets here to ensure some
# granularity of the resulting error messages (if any).
......
#
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
# Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019, 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.
......@@ -118,7 +118,6 @@ macro (gmx_c_flags)
GMX_TEST_CFLAG(CFLAGS_WARN_SUBSCRIPT "-Wno-char-subscripts" GMXC_CFLAGS)
endif()
GMX_TEST_CFLAG(CFLAGS_STRINGOP_TRUNCATION "-Werror=stringop-truncation" GMXC_CFLAGS)
GMX_TEST_CFLAG(CFLAGS_FORMAT_OVERFLOW "-Werror=format-overflow" GMXC_CFLAGS)
endif()
# new in gcc 4.5
GMX_TEST_CFLAG(CFLAGS_EXCESS_PREC "-fexcess-precision=fast" GMXC_CFLAGS_RELEASE)
......@@ -146,7 +145,6 @@ macro (gmx_c_flags)
if (CXXFLAGS_STRINGOP_TRUNCATION)
set(CXXFLAGS_NO_STRINGOP_TRUNCATION "-Wno-stringop-truncation")
endif()
GMX_TEST_CXXFLAG(CXXFLAGS_FORMAT_OVERFLOW "-Wformat-overflow" GMXC_CXXFLAGS)
endif()
# new in gcc 4.5
GMX_TEST_CXXFLAG(CXXFLAGS_EXCESS_PREC "-fexcess-precision=fast" GMXC_CXXFLAGS_RELEASE)
......
......@@ -74,9 +74,9 @@ function(gmx_manage_lmfit)
set(HAVE_LMFIT 1 CACHE INTERNAL "Is lmfit found?")
elseif(GMX_USE_LMFIT STREQUAL "EXTERNAL")
# Find an external lmfit library.
find_package(Lmfit ${GMX_LMFIT_MINIMUM_REQUIRED_VERSION})
if(NOT LMFIT_FOUND)
message(FATAL_ERROR "External lmfit could not be found, please adjust your pkg-config path to include the lmfit.pc file")
find_package(Lmfit ${GMX_LMFIT_REQUIRED_VERSION})
if(NOT LMFIT_FOUND OR LMFIT_VERSION VERSION_LESS GMX_LMFIT_REQUIRED_VERSION)
message(FATAL_ERROR "External lmfit >= ${GMX_LMFIT_REQUIRED_VERSION} could not be found, please adjust your pkg-config path to include the lmfit.pc file")
endif()
set(HAVE_LMFIT 1 CACHE INTERNAL "Is lmfit found?")
......
#
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
# Copyright (c) 2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
......@@ -168,7 +168,15 @@ list(APPEND GMX_CUDA_NVCC_FLAGS "${CUDA_HOST_COMPILER_OPTIONS}")
string(TOUPPER "${CMAKE_BUILD_TYPE}" _build_type)
gmx_check_if_changed(_cuda_nvcc_executable_or_flags_changed CUDA_NVCC_EXECUTABLE CUDA_NVCC_FLAGS CUDA_NVCC_FLAGS_${_build_type})
if(_cuda_nvcc_executable_or_flags_changed OR CUDA_HOST_COMPILER_CHANGED OR NOT GMX_NVCC_WORKS)
# We would like to be helpful and reject the host compiler with a
# clear error message at configure time, rather than let nvcc
# later reject the host compiler as not supported when the first
# CUDA source file is built. We've implemented that for current
# nvcc running on Unix-like systems, but e.g. changes to nvcc
# will further affect the limited portability of this checking
# code. Set the CMake variable GMX_NVCC_WORKS on if you want to
# bypass this check.
if((_cuda_nvcc_executable_or_flags_changed OR CUDA_HOST_COMPILER_CHANGED OR NOT GMX_NVCC_WORKS) AND NOT WIN32)
message(STATUS "Check for working NVCC/C compiler combination")
execute_process(COMMAND ${CUDA_NVCC_EXECUTABLE} -ccbin ${CUDA_HOST_COMPILER} -c ${CUDA_NVCC_FLAGS} ${CUDA_NVCC_FLAGS_${_build_type}} ${CMAKE_SOURCE_DIR}/cmake/TestCUDA.cu
RESULT_VARIABLE _cuda_test_res
......@@ -177,8 +185,9 @@ if(_cuda_nvcc_executable_or_flags_changed OR CUDA_HOST_COMPILER_CHANGED OR NOT G
OUTPUT_STRIP_TRAILING_WHITESPACE)
if(${_cuda_test_res})
message(${_cuda_test_err})
message(STATUS "Check for working NVCC/C compiler combination - broken")
message(STATUS "${CUDA_NVCC_EXECUTABLE} standard output: '${_cuda_test_out}'")
message(STATUS "${CUDA_NVCC_EXECUTABLE} standard error: '${_cuda_test_err}'")
if(${_cuda_test_err} MATCHES "nsupported")
message(FATAL_ERROR "NVCC/C compiler combination does not seem to be supported. CUDA frequently does not support the latest versions of the host compiler, so you might want to try an earlier C/C++ compiler version and make sure your CUDA compiler and driver are as recent as possible.")
else()
......
#
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2012,2013,2014,2015,2018, by the GROMACS development team, led by
# Copyright (c) 2012,2013,2014,2015,2018,2019, 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.
......@@ -64,6 +64,13 @@ add_definitions(${OpenCL_DEFINITIONS})
include_directories(SYSTEM ${OpenCL_INCLUDE_DIRS})
# Ensure the OpenCL implementation is 64-bit, because we only support that;
# Note that this can only be revised if the cl_mem size assumptions made
# (originally in pme-gpu-types.h) are relieved.
if (NOT CMAKE_SIZEOF_VOID_P EQUAL 8)
message(FATAL_ERROR "The OpenCL implementation is only supported on 64-bit platforms.")
endif()
set(GMX_OPENCL_NB_CLUSTER_SIZE 8 CACHE STRING "Cluster size used by nonbonded OpenCL kernel. Set to 4 for Intel GPUs.")
mark_as_advanced(GMX_OPENCL_NB_CLUSTER_SIZE)
......
#
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2017,2018, by the GROMACS development team, led by
# Copyright (c) 2017,2018,2019, 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.
......@@ -58,14 +58,19 @@ macro(find_power_vsx_toolchain_flags TOOLCHAIN_C_FLAGS_VARIABLE TOOLCHAIN_CXX_FL
# VSX uses the same function API as Altivec/VMX, so make sure we tune for the current CPU and not VMX.
# By putting these flags here rather than in the general compiler flags file we can safely assume
# that we are at least on Power7 since that is when VSX appeared.
# NOTE: Enabling instruction fusion on Power8/9 using -mpower8-fusion/-mpower9-fusion
# seems to produce buggy code (see #2747, #2746, #2734).
# Note that instruction fusion does have considerable performance benefits
# (up to 8% measured with gcc 8) if the issue is resolved the flag can be re-enabled.
gmx_run_cpu_detection(brand)
if(CPU_DETECTION_BRAND MATCHES "POWER7")
gmx_test_cflag(GNU_C_VSX_POWER7 "-mcpu=power7 -mtune=power7" ${TOOLCHAIN_C_FLAGS_VARIABLE})
gmx_test_cflag(GNU_CXX_VSX_POWER7 "-mcpu=power7 -mtune=power7" ${TOOLCHAIN_CXX_FLAGS_VARIABLE})
elseif(CPU_DETECTION_BRAND MATCHES "POWER8")
# Enable power8 vector extensions on such platforms.
gmx_test_cflag(GNU_C_VSX_POWER8 "-mcpu=power8 -mpower8-vector -mpower8-fusion" ${TOOLCHAIN_C_FLAGS_VARIABLE})
gmx_test_cflag(GNU_CXX_VSX_POWER8 "-mcpu=power8 -mpower8-vector -mpower8-fusion" ${TOOLCHAIN_CXX_FLAGS_VARIABLE})
gmx_test_cflag(GNU_C_VSX_POWER8 "-mcpu=power8 -mpower8-vector" ${TOOLCHAIN_C_FLAGS_VARIABLE})
gmx_test_cflag(GNU_CXX_VSX_POWER8 "-mcpu=power8 -mpower8-vector" ${TOOLCHAIN_CXX_FLAGS_VARIABLE})
elseif(CPU_DETECTION_BRAND MATCHES "POWER9")
# Enable power9 vector extensions on such platforms.
# TODO consider whether adding " -mpower9-vector -mpower9-fusion"
......
#
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2014,2015,2016,2017,2018, by the GROMACS development team, led by
# Copyright (c) 2014,2015,2016,2017,2018,2019, 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.
......@@ -82,7 +82,6 @@
# This ID is used for the source code tarball.
# GMX_MANUAL_DOI_ID
# Same as above, but for the reference manual.
# Setting and retrieving of those variables is handled in gmxCheckReleaseDOI.cmake
# They are collected into a single section below.
# The following variables are set based on these:
# GMX_VERSION String composed from GMX_VERSION_* numeric variables
......@@ -196,7 +195,7 @@
# 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 2019)
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
......@@ -241,7 +240,7 @@ set(REGRESSIONTEST_BRANCH "refs/heads/release-2019")
# 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 "1271a74bfe91028b7f184866d5aee98e" CACHE INTERNAL "MD5 sum of the regressiontests tarball for this GROMACS version")
set(REGRESSIONTEST_MD5SUM "36103a0078bf9a802e16ec982b4e5c4c" CACHE INTERNAL "MD5 sum of the regressiontests tarball for this GROMACS version")
math(EXPR GMX_VERSION_NUMERIC
"${GMX_VERSION_MAJOR}*10000 + ${GMX_VERSION_PATCH}")
......@@ -258,8 +257,8 @@ endif()
# from Zenodo for the manual and source code
# Has to be done by hand before every final release
# Use force to override anything given as a cmake command line input
set(GMX_MANUAL_DOI "10.5281/zenodo.2424486" CACHE INTERNAL "reserved doi for GROMACS manual" FORCE)
set(GMX_SOURCE_DOI "10.5281/zenodo.2424363" CACHE INTERNAL "reserved doi for GROMACS source code" FORCE)
set(GMX_MANUAL_DOI "10.5281/zenodo.2564761" CACHE INTERNAL "reserved doi for GROMACS manual" FORCE)
set(GMX_SOURCE_DOI "10.5281/zenodo.2564764" CACHE INTERNAL "reserved doi for GROMACS source code" FORCE)
#####################################################################
# git version info management
......
gromacs (2019.1-1) unstable; urgency=medium
* New upstream bugfix release.
* On x32 only, set openmpi tests to non-failing. They pass, but as of
openmpi >= 3.1.3~rc1, timeout on teardown. 3.1.2 works cleanly.
-- Nicholas Breen <nbreen@debian.org> Sun, 17 Feb 2019 09:22:14 -0800
gromacs (2019-2) unstable; urgency=medium
* Fix error in update-alternatives call for bash completion.
......
......@@ -174,12 +174,12 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
(cd build/openmpi ; LD_LIBRARY_PATH=$(CURDIR)/build/openmpi/lib \
OMPI_MCA_plm_rsh_agent=/bin/false \
OMPI_MCA_rmaps_base_oversubscribe=1 \
ctest -V || dpkg-architecture -i hurd-i386 )
ctest -V || dpkg-architecture -i hurd-i386 || dpkg-architecture -i x32 )
$(MAKE) -C build/openmpi-dp tests
(cd build/openmpi-dp ; LD_LIBRARY_PATH=$(CURDIR)/build/openmpi-dp/lib \
OMPI_MCA_plm_rsh_agent=/bin/false \
OMPI_MCA_rmaps_base_oversubscribe=1 \
ctest -V || dpkg-architecture -i hurd-i386 )
ctest -V || dpkg-architecture -i hurd-i386 || dpkg-architecture -i x32 )
endif
touch $@
......
#
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2014,2015,2016,2017,2018, by the GROMACS development team, led by
# Copyright (c) 2014,2015,2016,2017,2018,2019, 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.
......@@ -367,6 +367,7 @@ if (SPHINX_FOUND)
how-to/visualize.rst
install-guide/index.rst
release-notes/index.rst
release-notes/2019/2019.1.rst
release-notes/2019/major/highlights.rst
release-notes/2019/major/features.rst
release-notes/2019/major/performance.rst
......@@ -376,6 +377,7 @@ if (SPHINX_FOUND)
release-notes/2019/major/deprecated-functionality.rst
release-notes/2019/major/portability.rst
release-notes/2019/major/miscellaneous.rst
release-notes/2018/2018.6.rst
release-notes/2018/2018.5.rst
release-notes/2018/2018.4.rst
release-notes/2018/2018.3.rst
......
......@@ -203,7 +203,8 @@ version for |Gromacs| code as used as the host compiler for nvcc.
To make it possible to use other accelerators, |Gromacs| also includes
OpenCL_ support. The minimum OpenCL version required is
|REQUIRED_OPENCL_MIN_VERSION|. The current OpenCL implementation is recommended for
|REQUIRED_OPENCL_MIN_VERSION| and only 64-bit implementations are supported.
The current OpenCL implementation is recommended for
use with GCN-based AMD GPUs, and on Linux we recommend the ROCm runtime.
Intel integrated GPUs are supported with the Neo drivers.
OpenCL is also supported with NVIDIA GPUs, but using
......@@ -212,7 +213,8 @@ recommended. Also note that there are performance limitations (inherent
to the NVIDIA OpenCL runtime).
It is not possible to configure both CUDA and OpenCL
support in the same build of |Gromacs|, nor to support both
Intel and other vendors' GPUs with OpenCL.
Intel and other vendors' GPUs with OpenCL. A 64-bit implementation
of OpenCL is required and therefore OpenCL is only supported on 64-bit platforms.
.. _mpi-support:
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANADOCK" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-ANADOCK" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-anadock \- Cluster structures from Autodock runs
.
......@@ -95,6 +95,6 @@ Maximum RMSD/distance for belonging to the same cluster
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
.\" Generated by docutils manpage writer.
.
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANAEIG" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-ANAEIG" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-anaeig \- Analyze eigenvectors/normal modes
.
......@@ -249,6 +249,6 @@ Number of eigenvalues to skip when computing the entropy due to the quasi harmon
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
.\" Generated by docutils manpage writer.
.
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANALYZE" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-ANALYZE" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-analyze \- Analyze data sets
.
......@@ -282,6 +282,6 @@ Time where to end the exponential fit of the correlation function, \-1 is until
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
.\" Generated by docutils manpage writer.
.
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANGLE" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-ANGLE" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-angle \- Calculate distributions and correlations for angles and dihedrals
.
......@@ -177,6 +177,6 @@ Counting transitions only works for dihedrals with multiplicity 3
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
.\" Generated by docutils manpage writer.
.
.\" Man page generated from reStructuredText.
.
.TH "GMX-AWH" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-AWH" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-awh \- Extract data from an accelerated weight histogram (AWH) run
.
......@@ -108,6 +108,6 @@ Print free energy output in units of kT instead of kJ/mol
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
.\" Generated by docutils manpage writer.
.
.\" Man page generated from reStructuredText.
.
.TH "GMX-BAR" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-BAR" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-bar \- Calculate free energy difference estimates through Bennett's acceptance ratio
.
......@@ -229,6 +229,6 @@ Whether to linearly extrapolate dH/dl values to use as energies
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
.\" Generated by docutils manpage writer.
.
.\" Man page generated from reStructuredText.
.
.TH "GMX-BUNDLE" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-BUNDLE" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-bundle \- Analyze bundles of axes, e.g., helices
.
......@@ -148,6 +148,6 @@ Use the \fIz\fP\-axis as reference instead of the average axis
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
.\" Generated by docutils manpage writer.
.
.\" Man page generated from reStructuredText.
.
.TH "GMX-CHECK" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-CHECK" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-check \- Check and compare files
.
......@@ -150,6 +150,6 @@ Last energy term to compare (if not given all are tested). It makes sense to go
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
.\" Generated by docutils manpage writer.
.
.\" Man page generated from reStructuredText.
.
.TH "GMX-CHI" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-CHI" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-chi \- Calculate everything you want to know about chi and other dihedrals
.
......@@ -276,6 +276,6 @@ Rotamers with multiplicity 2 are printed in \fBchi.log\fP as if they had multipl
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
.\" Generated by docutils manpage writer.
.
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.TH "GMX-CLUSTER" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-CLUSTER" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-cluster \- Cluster structures
.
......@@ -293,6 +293,6 @@ PBC check
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-CLUSTSIZE" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-CLUSTSIZE" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-clustsize \- Calculate size distributions of atomic clusters
.
......@@ -163,6 +163,6 @@ RGB values for the color of the highest occupied cluster size
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-CONFRMS" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-CONFRMS" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-confrms \- Fit two structures and calculates the RMSD
.
......@@ -119,6 +119,6 @@ Output B\-factors from atomic MSD values
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-CONVERT-TPR" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-CONVERT-TPR" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-convert-tpr \- Make a modifed run-input file
.
......@@ -101,6 +101,6 @@ Set the charges of a group (from the index) to zero
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-COVAR" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-COVAR" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-covar \- Calculate and diagonalize the covariance matrix
.
......@@ -159,6 +159,6 @@ Apply corrections for periodic boundary conditions
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-CURRENT" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-CURRENT" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-current \- Calculate dielectric constants and current autocorrelation function
.
......@@ -166,6 +166,6 @@ Temperature for calculating epsilon.
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-DENSITY" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-DENSITY" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-density \- Calculate the density of the system
.
......@@ -192,6 +192,6 @@ When calculating electron densities, atomnames are used instead of types. This i
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-DENSMAP" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-DENSMAP" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-densmap \- Calculate 2D planar or axial-radial density maps
.
......@@ -165,6 +165,6 @@ Maximum density in output (0 means calculate it)
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-DENSORDER" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-DENSORDER" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-densorder \- Calculate surface fluctuations
.
......@@ -137,6 +137,6 @@ Number of Height levels in 2D \- XPixMaps
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-DIELECTRIC" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-DIELECTRIC" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-dielectric \- Calculate frequency dependent dielectric constants
.
......@@ -163,6 +163,6 @@ Number of points for smoothing
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-DIPOLES" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-DIPOLES" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-dipoles \- Compute the total dipole plus fluctuations
.
......@@ -243,6 +243,6 @@ Time where to end the exponential fit of the correlation function, \-1 is until
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-DISRE" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-DISRE" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-disre \- Analyze distance restraints
.
......@@ -148,6 +148,6 @@ Use inverse third power averaging or linear for matrix output
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-DISTANCE" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-DISTANCE" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-distance \- Calculate distances between pairs of positions
.
......@@ -159,6 +159,6 @@ Bin width for histogramming
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-DO_DSSP" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-DO_DSSP" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-do_dssp \- Assign secondary structure and calculate solvent accessible surface area
.
......@@ -160,6 +160,6 @@ DSSP major version. Syntax changed with version 2
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-DOS" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-DOS" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-dos \- Analyze density of states and properties based on that
.
......@@ -156,6 +156,6 @@ This program needs a lot of memory: total usage equals the number of atoms times
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-DUMP" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-DUMP" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-dump \- Make binary files human readable
.
......@@ -112,6 +112,6 @@ Position restraint output from \-sys \-s is broken
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-DYECOUPL" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-DYECOUPL" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-dyecoupl \- Extract dye dynamics from trajectories
.
......@@ -130,6 +130,6 @@ Foerster radius including kappa^2=2/3 in nm
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-DYNDOM" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-DYNDOM" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-dyndom \- Interpolate and extrapolate structure rotations
.
......@@ -114,6 +114,6 @@ Last atom of the arrow vector
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-EDITCONF" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-EDITCONF" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-editconf \- Convert and manipulates structure files
.
......@@ -266,6 +266,6 @@ For complex molecules, the periodicity removal routine may break down, in that c
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-ENECONV" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-ENECONV" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-eneconv \- Convert energy files
.
......@@ -121,6 +121,6 @@ When combining trajectories the sigma and E^2 (necessary for statistics) are not
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-ENEMAT" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-ENEMAT" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-enemat \- Extract an energy matrix from an energy file
.
......@@ -175,6 +175,6 @@ reference temperature for free energy calculation
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-ENERGY" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-ENERGY" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-energy \- Writes energies to xvg files and display averages
.
......@@ -307,6 +307,6 @@ Time where to end the exponential fit of the correlation function, \-1 is until
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-FILTER" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-FILTER" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-filter \- Frequency filter trajectories, useful for making smooth movies
.
......@@ -125,6 +125,6 @@ Fit all frames to a reference structure
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-FREEVOLUME" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-FREEVOLUME" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-freevolume \- Calculate free volume
.
......@@ -149,6 +149,6 @@ Number of probe insertions per cubic nm to try for each frame in the trajectory.
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-GANGLE" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-GANGLE" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-gangle \- Calculate angles
.
......@@ -187,6 +187,6 @@ Second analysis/vector selection
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-GENCONF" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-GENCONF" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-genconf \- Multiply a conformation in 'random' orientations
.
......@@ -111,6 +111,6 @@ The program should allow for random displacement of lattice points.
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-GENION" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-GENION" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-genion \- Generate monoatomic ions on energetically favorable positions
.
......@@ -132,6 +132,6 @@ If you specify a salt concentration existing ions are not taken into account. In
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-GENRESTR" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-GENRESTR" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-genrestr \- Generate position restraints or distance restraints for index groups
.
......@@ -127,6 +127,6 @@ Generate a constraint matrix rather than distance restraints. Constraints of typ
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-GROMPP" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-GROMPP" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-grompp \- Make a run input file
.
......@@ -240,6 +240,6 @@ Renumber atomtypes and minimize number of atomtypes
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-GYRATE" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-GYRATE" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-gyrate \- Calculate the radius of gyration
.
......@@ -145,6 +145,6 @@ Time where to end the exponential fit of the correlation function, \-1 is until
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-H2ORDER" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-H2ORDER" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-h2order \- Compute the orientation of water molecules
.
......@@ -114,6 +114,6 @@ The program assigns whole water molecules to a slice, based on the first atom of
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-HBOND" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-HBOND" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-hbond \- Compute and analyze hydrogen bonds
.
......@@ -268,6 +268,6 @@ The option \fB\-sel\fP that used to work on selected hbonds is out of order, and
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-HELIX" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-HELIX" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-helix \- Calculate basic properties of alpha helices
.
......@@ -152,6 +152,6 @@ Last residue in helix
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-HELIXORIENT" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-HELIXORIENT" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-helixorient \- Calculate local pitch/bending/rotation/orientation inside helices
.
......@@ -138,6 +138,6 @@ Calculate incremental rather than total rotation/tilt.
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-HELP" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-HELP" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-help \- Print help information
.
......@@ -36,6 +36,6 @@ level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-HYDORDER" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-HYDORDER" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-hydorder \- Compute tetrahedrality parameters around a given atom
.
......@@ -124,6 +124,6 @@ Number of Height levels in 2D \- XPixMaps
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-INSERT-MOLECULES" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-INSERT-MOLECULES" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-insert-molecules \- Insert molecules into existing vacancies
.
......@@ -157,6 +157,6 @@ Rotate inserted molecules randomly: xyz, z, none
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-LIE" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-LIE" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-lie \- Estimate free energy from linear combinations
.
......@@ -109,6 +109,6 @@ Name of the ligand in the energy file
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
.\" Generated by docutils manpage writer.
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.TH "GMX-MAKE_EDI" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-MAKE_EDI" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-make_edi \- Generate input files for essential dynamics sampling
.
......@@ -284,6 +284,6 @@ Constant force flooding: manually set the forces for the eigenvectors selected w
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-MAKE_NDX" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-MAKE_NDX" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-make_ndx \- Make index files
.
......@@ -103,6 +103,6 @@ Duplicate all index groups with an offset of \-natoms
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-MDMAT" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-MDMAT" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-mdmat \- Calculate residue contact maps
.
......@@ -110,6 +110,6 @@ Discretize distance in this number of levels
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-MDRUN" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-MDRUN" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-mdrun \- Perform a simulation, do a normal mode analysis or an energy minimization
.
......@@ -452,6 +452,6 @@ Seed for replica exchange, \-1 is generate a seed
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-MINDIST" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-MINDIST" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-mindist \- Calculate the minimum distance between two groups
.
......@@ -161,6 +161,6 @@ Write residue names
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-MK_ANGNDX" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-MK_ANGNDX" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-mk_angndx \- Generate index files for 'gmx angle'
.
......@@ -81,6 +81,6 @@ Ignore angles with atoms with mass < 1.5 and magnitude of their charge less than
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-MORPH" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-MORPH" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-morph \- Interpolate linearly between conformations
.
......@@ -114,6 +114,6 @@ Do a least squares fit of the second to the first structure before interpolating
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-MSD" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-MSD" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-msd \- Calculates mean square displacements
.
......@@ -178,6 +178,6 @@ End time for fitting the MSD (ps), \-1 is 90%
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-NMEIG" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-NMEIG" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-nmeig \- Diagonalize the Hessian for normal mode analysis
.
......@@ -159,6 +159,6 @@ Width (sigma) of the gaussian peaks (1/cm) when generating a spectrum
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-NMENS" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-NMENS" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-nmens \- Generate an ensemble of structures from the normal modes
.
......@@ -106,6 +106,6 @@ Last eigenvector to use (\-1 is till the last)
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-NMR" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-NMR" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-nmr \- Analyze nuclear magnetic resonance properties from an energy file
.
......@@ -154,6 +154,6 @@ Also plot the eigenvectors with \fB\-oten\fP
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-NMTRAJ" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-NMTRAJ" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-nmtraj \- Generate a virtual oscillating trajectory from an eigenvector
.
......@@ -103,6 +103,6 @@ Number of frames to generate
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-ORDER" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-ORDER" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-order \- Compute the order parameter per atom for carbon tails
.
......@@ -160,6 +160,6 @@ Compute distance from a reference
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-PAIRDIST" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-PAIRDIST" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-pairdist \- Calculate pairwise distances between groups of positions
.
......@@ -167,6 +167,6 @@ Positions to calculate distances for
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-PDB2GMX" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-PDB2GMX" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-pdb2gmx \- Convert coordinate files to topology and FF-compliant coordinate files
.
......@@ -277,6 +277,6 @@ Use \&.rtp entry names as residue names
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-PME_ERROR" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-PME_ERROR" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-pme_error \- Estimate the error of using PME with a given input file
.
......@@ -95,6 +95,6 @@ Be loud and noisy
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-POLYSTAT" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-POLYSTAT" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-polystat \- Calculate static properties of polymers
.
......@@ -135,6 +135,6 @@ Plot average eigenvalues
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-POTENTIAL" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-POTENTIAL" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-potential \- Calculate the electrostatic potential across the box
.
......@@ -136,6 +136,6 @@ Discarding slices for integration should not be necessary.
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-PRINCIPAL" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-PRINCIPAL" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-principal \- Calculate principal axes of inertia for a group of atoms
.
......@@ -114,6 +114,6 @@ Dummy option to avoid empty array
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-RAMA" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-RAMA" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-rama \- Compute Ramachandran plots
.
......@@ -91,6 +91,6 @@ xvg plot formatting: xmgrace, xmgr, none
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-RDF" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-RDF" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-rdf \- Calculate radial distribution functions
.
......@@ -195,6 +195,6 @@ Selections to compute RDFs for from the reference
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-REPORT-METHODS" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-REPORT-METHODS" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-report-methods \- Write short summary about the simulation setup to a text file and/or to the standard output.
.
......@@ -74,6 +74,6 @@ Unformatted report output to file
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-RMS" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-RMS" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME
gmx-rms \- Calculate RMSDs with a reference structure and RMSD matrices
.
......@@ -208,6 +208,6 @@ Number of groups to compute RMS between
.sp
More information about GROMACS is available at <\fI\%http://www.gromacs.org/\fP>.
.SH COPYRIGHT
2018, GROMACS development team
2019, GROMACS development team
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.TH "GMX-RMSDIST" "1" "Dec 31, 2018" "2019" "GROMACS"
.TH "GMX-RMSDIST" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.SH NAME