Commit 26be3b24 authored by Nicholas Breen's avatar Nicholas Breen

New upstream version 2019.3

parent 26b188a1
......@@ -5,7 +5,7 @@ Installation guide
Introduction to building GROMACS
================================
These instructions pertain to building GROMACS 2019.1. You might also
These instructions pertain to building GROMACS 2019.3. 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-2019.1.tar.gz
cd gromacs-2019.1
tar xfz gromacs-2019.3.tar.gz
cd gromacs-2019.3
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-2019.1. We recommend to use the gcc
POWER architectures for GROMACS-2019.3. 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
......@@ -266,6 +266,9 @@ More specialized networks might depend on accelerations only available
in the vendor’s library. LAM-MPI might work, but since it has been
deprecated for years, it is not supported.
For example, depending on your actual MPI library, use "cmake
-DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DGMX_MPI=on".
CMake
-----
......@@ -439,8 +442,8 @@ 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-2019.1.tgz
cd gromacs-2019.1
tar xfz gromacs-2019.3.tgz
cd gromacs-2019.3
mkdir build-gromacs
cd build-gromacs
cmake ..
......@@ -1043,7 +1046,7 @@ 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-2019.1.tar.gz
http://gerrit.gromacs.org/download/regressiontests-2019.3.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
......
#
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2017, by the GROMACS development team, led by
# Copyright (c) 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.
......@@ -83,7 +83,7 @@ function(gmx_detect_avx_512_fma_units RESULT)
ERROR_QUIET)
if (RESULT_VAR EQUAL 0)
string(STRIP "${OUTPUT_VAR_TEMP}" OUTPUT_VAR)
set(${RESULT} ${OUTPUT_VAR_TEMP} CACHE INTERNAL "Result of test for number of AVX-512 FMA units")
set(${RESULT} ${OUTPUT_VAR} CACHE INTERNAL "Result of test for number of AVX-512 FMA units")
else()
message(STATUS "Could not identify number of AVX-512 units - detection program did run successfully")
set(${RESULT} -1 CACHE INTERNAL "Result of test for number of AVX-512 FMA units")
......
#
# 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.
......@@ -108,6 +108,7 @@ if(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
NO_CMAKE_PATH
NO_SYSTEM_ENVIRONMENT_PATH
NO_CMAKE_SYSTEM_PATH)
mark_as_advanced(ARMPL_INCLUDE_DIR)
if (ARMPL_INCLUDE_DIR)
set(GMX_FFT_ARMPL_FFTW3 1)
set(FFT_STATUS_MESSAGE "Using external FFT library - ARM Performance Library (FFTW3 compatibility mode)")
......
......@@ -177,7 +177,7 @@ gmx_check_if_changed(_cuda_nvcc_executable_or_flags_changed CUDA_NVCC_EXECUTABLE
# code. Set the CMake variable GMX_NVCC_WORKS on if you want to
# bypass this check.
if((_cuda_nvcc_executable_or_flags_changed OR CUDA_HOST_COMPILER_CHANGED OR NOT GMX_NVCC_WORKS) AND NOT WIN32)
message(STATUS "Check for working NVCC/C compiler combination")
message(STATUS "Check for working NVCC/C++ compiler combination with nvcc '${CUDA_NVCC_EXECUTABLE}'")
execute_process(COMMAND ${CUDA_NVCC_EXECUTABLE} -ccbin ${CUDA_HOST_COMPILER} -c ${CUDA_NVCC_FLAGS} ${CUDA_NVCC_FLAGS_${_build_type}} ${CMAKE_SOURCE_DIR}/cmake/TestCUDA.cu
RESULT_VARIABLE _cuda_test_res
OUTPUT_VARIABLE _cuda_test_out
......@@ -189,12 +189,12 @@ if((_cuda_nvcc_executable_or_flags_changed OR CUDA_HOST_COMPILER_CHANGED OR NOT
message(STATUS "${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.")
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++ compiler version and make sure your CUDA compiler and driver are as recent as possible.")
else()
message(FATAL_ERROR "CUDA compiler does not seem to be functional.")
endif()
elseif(NOT GMX_CUDA_TEST_COMPILER_QUIETLY)
message(STATUS "Check for working NVCC/C compiler combination - works")
message(STATUS "Check for working NVCC/C++ compiler combination - works")
set(GMX_NVCC_WORKS TRUE CACHE INTERNAL "Nvcc can compile a trivial test program")
endif()
endif() # GMX_CHECK_NVCC
......
......@@ -195,7 +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 1)
set(GMX_VERSION_PATCH 3)
# 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
......@@ -240,7 +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 "36103a0078bf9a802e16ec982b4e5c4c" CACHE INTERNAL "MD5 sum of the regressiontests tarball for this GROMACS version")
set(REGRESSIONTEST_MD5SUM "d60f1a930705248d9779f37325736af3" CACHE INTERNAL "MD5 sum of the regressiontests tarball for this GROMACS version")
math(EXPR GMX_VERSION_NUMERIC
"${GMX_VERSION_MAJOR}*10000 + ${GMX_VERSION_PATCH}")
......@@ -257,8 +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.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)
set(GMX_MANUAL_DOI "10.5281/zenodo.3243834" CACHE INTERNAL "reserved doi for GROMACS manual" FORCE)
set(GMX_SOURCE_DOI "10.5281/zenodo.3243833" CACHE INTERNAL "reserved doi for GROMACS source code" FORCE)
#####################################################################
# git version info management
......
......@@ -367,6 +367,8 @@ if (SPHINX_FOUND)
how-to/visualize.rst
install-guide/index.rst
release-notes/index.rst
release-notes/2019/2019.3.rst
release-notes/2019/2019.2.rst
release-notes/2019/2019.1.rst
release-notes/2019/major/highlights.rst
release-notes/2019/major/features.rst
......@@ -377,6 +379,7 @@ if (SPHINX_FOUND)
release-notes/2019/major/deprecated-functionality.rst
release-notes/2019/major/portability.rst
release-notes/2019/major/miscellaneous.rst
release-notes/2018/2018.7.rst
release-notes/2018/2018.6.rst
release-notes/2018/2018.5.rst
release-notes/2018/2018.4.rst
......@@ -595,24 +598,27 @@ if (SPHINX_FOUND)
else()
set(MANUAL_BUILD_IS_POSSIBLE OFF)
set(MANUAL_BUILD_NOT_POSSIBLE_REASON "Sphinx version ${EXPECTED_SPHINX_VERSION} is not available")
set(MANUAL_BUILD_NOT_POSSIBLE_REASON "Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available")
add_custom_target(webpage-sphinx
COMMAND ${CMAKE_COMMAND} -E echo
"HTML pages cannot be built because Sphinx version ${EXPECTED_SPHINX_VERSION} is not available"
"HTML pages cannot be built because Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available"
VERBATIM)
add_custom_target(install-guide
COMMAND ${CMAKE_COMMAND} -E echo
"INSTALL cannot be built because Sphinx version ${EXPECTED_SPHINX_VERSION} is not available"
"INSTALL cannot be built because Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available"
VERBATIM)
add_custom_target(man
COMMAND ${CMAKE_COMMAND} -E echo
"man pages cannot be built because Sphinx version ${EXPECTED_SPHINX_VERSION} is not available"
"man pages cannot be built because Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available"
VERBATIM)
add_custom_target(sphinx-create-texman
COMMAND ${CMAKE_COMMAND} -E echo
"Cannot prepare LaTeX input files because Sphinx version ${EXPECTED_SPHINX_VERSION} is not available"
"Cannot prepare LaTeX input files because Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available"
VERBATIM)
add_custom_target(manual
COMMAND ${CMAKE_COMMAND} -E echo
"manual cannot be built because Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is not available")
endif()
if (MAN_PAGE_DIR)
......@@ -641,7 +647,7 @@ if (NOT PYTHON_EXECUTABLE)
elseif (NOT SPHINX_FOUND)
# Hardly anything gets built if Sphinx is not available, so don't bother.
set(HTML_BUILD_IS_POSSIBLE OFF)
set(HTML_BUILD_NOT_POSSIBLE_REASON "Sphinx version ${EXPECTED_SPHINX_VERSION} is required")
set(HTML_BUILD_NOT_POSSIBLE_REASON "Sphinx expected minimum version ${EXPECTED_SPHINX_VERSION} is required")
endif()
if (NOT MANUAL_BUILD_IS_POSSIBLE)
list(APPEND HTML_BUILD_WARNINGS
......
......@@ -240,6 +240,10 @@ networks might depend on accelerations only available in the vendor's
library. LAM-MPI_ might work, but since it has
been deprecated for years, it is not supported.
For example, depending on your actual MPI library, use ``cmake
-DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DGMX_MPI=on``.
CMake
^^^^^
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANADOCK" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-ANADOCK" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-anadock \- Cluster structures from Autodock runs
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANAEIG" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-ANAEIG" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-anaeig \- Analyze eigenvectors/normal modes
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANALYZE" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-ANALYZE" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-analyze \- Analyze data sets
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANGLE" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-ANGLE" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-angle \- Calculate distributions and correlations for angles and dihedrals
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-AWH" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-AWH" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-awh \- Extract data from an accelerated weight histogram (AWH) run
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-BAR" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-BAR" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-bar \- Calculate free energy difference estimates through Bennett's acceptance ratio
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-BUNDLE" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-BUNDLE" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-bundle \- Analyze bundles of axes, e.g., helices
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CHECK" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-CHECK" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-check \- Check and compare files
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CHI" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-CHI" "1" "Jun 14, 2019" "2019.3" "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" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-CLUSTER" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-cluster \- Cluster structures
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CLUSTSIZE" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-CLUSTSIZE" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-clustsize \- Calculate size distributions of atomic clusters
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CONFRMS" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-CONFRMS" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-confrms \- Fit two structures and calculates the RMSD
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CONVERT-TPR" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-CONVERT-TPR" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-convert-tpr \- Make a modifed run-input file
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-COVAR" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-COVAR" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-covar \- Calculate and diagonalize the covariance matrix
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CURRENT" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-CURRENT" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-current \- Calculate dielectric constants and current autocorrelation function
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DENSITY" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-DENSITY" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-density \- Calculate the density of the system
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DENSMAP" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-DENSMAP" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-densmap \- Calculate 2D planar or axial-radial density maps
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DENSORDER" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-DENSORDER" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-densorder \- Calculate surface fluctuations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DIELECTRIC" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-DIELECTRIC" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-dielectric \- Calculate frequency dependent dielectric constants
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DIPOLES" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-DIPOLES" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-dipoles \- Compute the total dipole plus fluctuations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DISRE" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-DISRE" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-disre \- Analyze distance restraints
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DISTANCE" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-DISTANCE" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-distance \- Calculate distances between pairs of positions
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DO_DSSP" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-DO_DSSP" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-do_dssp \- Assign secondary structure and calculate solvent accessible surface area
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DOS" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-DOS" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-dos \- Analyze density of states and properties based on that
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DUMP" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-DUMP" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-dump \- Make binary files human readable
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DYECOUPL" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-DYECOUPL" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-dyecoupl \- Extract dye dynamics from trajectories
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DYNDOM" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-DYNDOM" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-dyndom \- Interpolate and extrapolate structure rotations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-EDITCONF" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-EDITCONF" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-editconf \- Convert and manipulates structure files
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ENECONV" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-ENECONV" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-eneconv \- Convert energy files
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ENEMAT" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-ENEMAT" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-enemat \- Extract an energy matrix from an energy file
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ENERGY" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-ENERGY" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-energy \- Writes energies to xvg files and display averages
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-FILTER" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-FILTER" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-filter \- Frequency filter trajectories, useful for making smooth movies
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-FREEVOLUME" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-FREEVOLUME" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-freevolume \- Calculate free volume
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-GANGLE" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-GANGLE" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-gangle \- Calculate angles
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-GENCONF" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-GENCONF" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-genconf \- Multiply a conformation in 'random' orientations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-GENION" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-GENION" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-genion \- Generate monoatomic ions on energetically favorable positions
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-GENRESTR" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-GENRESTR" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-genrestr \- Generate position restraints or distance restraints for index groups
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-GROMPP" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-GROMPP" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-grompp \- Make a run input file
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-GYRATE" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-GYRATE" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-gyrate \- Calculate the radius of gyration
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-H2ORDER" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-H2ORDER" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-h2order \- Compute the orientation of water molecules
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-HBOND" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-HBOND" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-hbond \- Compute and analyze hydrogen bonds
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-HELIX" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-HELIX" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-helix \- Calculate basic properties of alpha helices
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-HELIXORIENT" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-HELIXORIENT" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-helixorient \- Calculate local pitch/bending/rotation/orientation inside helices
.
......
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.TH "GMX-HELP" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-HELP" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-help \- Print help information
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.TH "GMX-HYDORDER" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-HYDORDER" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-hydorder \- Compute tetrahedrality parameters around a given atom
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.TH "GMX-INSERT-MOLECULES" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-INSERT-MOLECULES" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-insert-molecules \- Insert molecules into existing vacancies
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.TH "GMX-LIE" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-LIE" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-lie \- Estimate free energy from linear combinations
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.TH "GMX-MAKE_EDI" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-MAKE_EDI" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-make_edi \- Generate input files for essential dynamics sampling
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.TH "GMX-MAKE_NDX" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-MAKE_NDX" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-make_ndx \- Make index files
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.TH "GMX-MDMAT" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-MDMAT" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-mdmat \- Calculate residue contact maps
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.TH "GMX-MDRUN" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-MDRUN" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-mdrun \- Perform a simulation, do a normal mode analysis or an energy minimization
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......@@ -432,7 +432,7 @@ Keep and number checkpoint files
Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names
.TP
.B \fB\-nsteps\fP <int> (\-2)
Run this number of steps, overrides .mdp file option (\-1 means infinite, \-2 means use mdp option, smaller is invalid)
Run this number of steps (\-1 means infinite, \-2 means use mdp option, smaller is invalid)
.TP
.B \fB\-maxh\fP <real> (\-1)
Terminate after 0.99 times this time (hours)
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.TH "GMX-MINDIST" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-MINDIST" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-mindist \- Calculate the minimum distance between two groups
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.TH "GMX-MK_ANGNDX" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-MK_ANGNDX" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-mk_angndx \- Generate index files for 'gmx angle'
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.TH "GMX-MORPH" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-MORPH" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-morph \- Interpolate linearly between conformations
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.TH "GMX-MSD" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-MSD" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-msd \- Calculates mean square displacements
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.TH "GMX-NMEIG" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-NMEIG" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME
gmx-nmeig \- Diagonalize the Hessian for normal mode analysis
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.TH "GMX-NMENS" "1" "Feb 15, 2019" "2019.1" "GROMACS"
.TH "GMX-NMENS" "1" "Jun 14, 2019" "2019.3" "GROMACS"
.SH NAME