Upgrading to GitLab 11.10.0. Expect errors and see debian-infrastructure-announce@lists.debian.org for further information.

Commit 8fba444b authored by Nicholas Breen's avatar Nicholas Breen

Update upstream source from tag 'upstream/2018.4'

Update to upstream version '2018.4'
with Debian dir 88f05be939767afd26b8693981b93be62f04efc8
parents 3e4c2718 dcd3f1ba
......@@ -5,7 +5,7 @@ Installation guide
Introduction to building GROMACS
================================
These instructions pertain to building GROMACS 2018.3. You might also
These instructions pertain to building GROMACS 2018.4. 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-2018.3.tar.gz
cd gromacs-2018.3
tar xfz gromacs-2018.4.tar.gz
cd gromacs-2018.4
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-2018.3. We recommend to use the gcc compiler
architectures for GROMACS-2018.4. 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-2018.3.tgz
cd gromacs-2018.3
tar xfz gromacs-2018.4.tgz
cd gromacs-2018.4
mkdir build-gromacs
cd build-gromacs
cmake ..
......@@ -994,7 +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-2018.3.tar.gz
http://gerrit.gromacs.org/download/regressiontests-2018.4.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) 2015,2016,2017, by the GROMACS development team, led by
# Copyright (c) 2015,2016,2017,2018, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
......@@ -44,6 +44,7 @@ extra_options = {
'release-with-assert': Option.simple,
'release-with-debug-info': Option.simple,
'asan': Option.simple,
'tng' : Option.bool,
'mkl': Option.simple,
'fftpack': Option.simple,
'double': Option.simple,
......@@ -54,7 +55,8 @@ extra_options = {
'openmp': Option.bool,
'nranks': Option.string,
'npme': Option.string,
'gpu_id': Option.string
'gpu_id': Option.string,
'hwloc': Option.bool
}
extra_projects = [Project.REGRESSIONTESTS]
......@@ -112,6 +114,8 @@ def do_build(context):
cmake_opts['GMX_MPI'] = 'ON'
if context.opts.openmp is False:
cmake_opts['GMX_OPENMP'] = 'OFF'
if context.opts.tng is False:
cmake_opts['GMX_USE_TNG'] = 'OFF'
if context.opts.mkl:
cmake_opts['GMX_FFT_LIBRARY'] = 'mkl'
......@@ -121,6 +125,9 @@ def do_build(context):
cmake_opts['GMX_EXTERNAL_BLAS'] = 'ON'
cmake_opts['GMX_EXTERNAL_LAPACK'] = 'ON'
if context.opts.hwloc is False:
cmake_opts['GMX_HWLOC'] = 'OFF'
if context.opts.x11:
cmake_opts['GMX_X11'] = 'ON'
......
......@@ -11,7 +11,7 @@
# Test on ARM v7
# Test ARM_NEON SIMD
gcc-4.8 simd=ARM_NEON release-with-assert
gcc-4.8 simd=ARM_NEON no-hwloc release-with-assert
# Test on ARM v8
# Test ARM_NEON_ASIMD SIMD
......@@ -29,7 +29,8 @@ gcc-7 mpi no-openmp fftpack mdrun-only
icc-18 npme=1 nranks=2 no-openmp double fftpack release simd=none
# Test CUDA build on a slave with no CUDA devices
gcc-4.9 gpu cuda-7.0 openmp release-with-assert
# Test without TNG support
gcc-4.9 gpu cuda-7.0 openmp no-tng release-with-assert
# Test non-default GMX_PREFER_STATIC_LIBS behavior
# TODO enable this
......@@ -65,7 +66,6 @@ icc-16 msvc-2015 fftpack simd=avx2_256 release
# Add SIMD + OpenMP + CUDA asan build
# Add OpenMP + CUDA + device sharing TSAN build
# Re-enable Phi build (FIXME: do we still care?)
# Test without TNG support
# Test without hwloc support
# Test with NVML support
# Test statically linked hwloc support (if/when it can work well)
......
......@@ -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 3)
set(GMX_VERSION_PATCH 4)
# 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 3)
set(LIBRARY_SOVERSION_MINOR 4)
set(LIBRARY_VERSION ${LIBRARY_SOVERSION_MAJOR}.${LIBRARY_SOVERSION_MINOR}.0)
#####################################################################
......@@ -231,7 +231,7 @@ set(REGRESSIONTEST_BRANCH "refs/heads/release-2018")
# 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 "368aabf0eb4e6fbc9abb7961475f66de" CACHE INTERNAL "MD5 sum of the regressiontests tarball for this GROMACS version")
set(REGRESSIONTEST_MD5SUM "eb9b4e884e671ec2e1a62cc4d88a5533" 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/2018/2018.4.rst
release-notes/2018/2018.3.rst
release-notes/2018/2018.2.rst
release-notes/2018/2018.1.rst
......@@ -165,6 +166,7 @@ if (SPHINX_FOUND)
user-guide/file-formats.rst
user-guide/cmdline.rst
user-guide/environment-variables.rst
user-guide/security.rst
user-guide/terminology.rst
user-guide/plotje.gif
user-guide/xvgr.gif
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANADOCK" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-ANADOCK" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-anadock \- Cluster structures from Autodock runs
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANAEIG" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-ANAEIG" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-anaeig \- Analyze eigenvectors/normal modes
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANALYZE" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-ANALYZE" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-analyze \- Analyze data sets
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANGLE" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-ANGLE" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-angle \- Calculate distributions and correlations for angles and dihedrals
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-AWH" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-AWH" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-awh \- Extract data from an accelerated weight histogram (AWH) run
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-BAR" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-BAR" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-bar \- Calculate free energy difference estimates through Bennett's acceptance ratio
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-BUNDLE" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-BUNDLE" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-bundle \- Analyze bundles of axes, e.g., helices
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CHECK" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-CHECK" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-check \- Check and compare files
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CHI" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-CHI" "1" "Nov 12, 2018" "2018.4" "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" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-CLUSTER" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-cluster \- Cluster structures
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CLUSTSIZE" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-CLUSTSIZE" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-clustsize \- Calculate size distributions of atomic clusters
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CONFRMS" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-CONFRMS" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-confrms \- Fit two structures and calculates the RMSD
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CONVERT-TPR" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-CONVERT-TPR" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-convert-tpr \- Make a modifed run-input file
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-COVAR" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-COVAR" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-covar \- Calculate and diagonalize the covariance matrix
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CURRENT" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-CURRENT" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-current \- Calculate dielectric constants and current autocorrelation function
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DENSITY" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-DENSITY" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-density \- Calculate the density of the system
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DENSMAP" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-DENSMAP" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-densmap \- Calculate 2D planar or axial-radial density maps
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DENSORDER" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-DENSORDER" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-densorder \- Calculate surface fluctuations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DIELECTRIC" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-DIELECTRIC" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-dielectric \- Calculate frequency dependent dielectric constants
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DIPOLES" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-DIPOLES" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-dipoles \- Compute the total dipole plus fluctuations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DISRE" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-DISRE" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-disre \- Analyze distance restraints
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DISTANCE" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-DISTANCE" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-distance \- Calculate distances between pairs of positions
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DO_DSSP" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-DO_DSSP" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-do_dssp \- Assign secondary structure and calculate solvent accessible surface area
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DOS" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-DOS" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-dos \- Analyze density of states and properties based on that
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DUMP" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-DUMP" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-dump \- Make binary files human readable
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DYECOUPL" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-DYECOUPL" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-dyecoupl \- Extract dye dynamics from trajectories
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-DYNDOM" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-DYNDOM" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-dyndom \- Interpolate and extrapolate structure rotations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-EDITCONF" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-EDITCONF" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-editconf \- Convert and manipulates structure files
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-ENECONV" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-ENECONV" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-eneconv \- Convert energy files
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ENEMAT" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-ENEMAT" "1" "Nov 12, 2018" "2018.4" "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" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-ENERGY" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-energy \- Writes energies to xvg files and display averages
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-FILTER" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-FILTER" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-filter \- Frequency filter trajectories, useful for making smooth movies
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-FREEVOLUME" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-FREEVOLUME" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-freevolume \- Calculate free volume
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-GANGLE" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-GANGLE" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-gangle \- Calculate angles
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-GENCONF" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-GENCONF" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-genconf \- Multiply a conformation in 'random' orientations
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-GENION" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-GENION" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-genion \- Generate monoatomic ions on energetically favorable positions
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-GENRESTR" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-GENRESTR" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-genrestr \- Generate position restraints or distance restraints for index groups
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-GROMPP" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-GROMPP" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-grompp \- Make a run input file
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-GYRATE" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-GYRATE" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-gyrate \- Calculate the radius of gyration
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-H2ORDER" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-H2ORDER" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-h2order \- Compute the orientation of water molecules
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-HBOND" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-HBOND" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-hbond \- Compute and analyze hydrogen bonds
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-HELIX" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-HELIX" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-helix \- Calculate basic properties of alpha helices
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-HELIXORIENT" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-HELIXORIENT" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-helixorient \- Calculate local pitch/bending/rotation/orientation inside helices
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-HELP" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-HELP" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-help \- Print help information
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-HYDORDER" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-HYDORDER" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-hydorder \- Compute tetrahedrality parameters around a given atom
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-INSERT-MOLECULES" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-INSERT-MOLECULES" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-insert-molecules \- Insert molecules into existing vacancies
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-LIE" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-LIE" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-lie \- Estimate free energy from linear combinations
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-MAKE_EDI" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-MAKE_EDI" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-make_edi \- Generate input files for essential dynamics sampling
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-MAKE_NDX" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-MAKE_NDX" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-make_ndx \- Make index files
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-MDMAT" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-MDMAT" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-mdmat \- Calculate residue contact maps
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-MDRUN" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-MDRUN" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-mdrun \- Perform a simulation, do a normal mode analysis or an energy minimization
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-MINDIST" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-MINDIST" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-mindist \- Calculate the minimum distance between two groups
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-MK_ANGNDX" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-MK_ANGNDX" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-mk_angndx \- Generate index files for 'gmx angle'
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-MORPH" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-MORPH" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-morph \- Interpolate linearly between conformations
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-MSD" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-MSD" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-msd \- Calculates mean square displacements
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-NMEIG" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-NMEIG" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-nmeig \- Diagonalize the Hessian for normal mode analysis
.
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.TH "GMX-NMENS" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-NMENS" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-nmens \- Generate an ensemble of structures from the normal modes
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.TH "GMX-NMR" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-NMR" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-nmr \- Analyze nuclear magnetic resonance properties from an energy file
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.TH "GMX-NMTRAJ" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-NMTRAJ" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-nmtraj \- Generate a virtual oscillating trajectory from an eigenvector
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.TH "GMX-ORDER" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-ORDER" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-order \- Compute the order parameter per atom for carbon tails
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.TH "GMX-PAIRDIST" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-PAIRDIST" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-pairdist \- Calculate pairwise distances between groups of positions
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.TH "GMX-PDB2GMX" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-PDB2GMX" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-pdb2gmx \- Convert coordinate files to topology and FF-compliant coordinate files
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.TH "GMX-PME_ERROR" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-PME_ERROR" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-pme_error \- Estimate the error of using PME with a given input file
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.TH "GMX-POLYSTAT" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-POLYSTAT" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-polystat \- Calculate static properties of polymers
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.TH "GMX-POTENTIAL" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.TH "GMX-POTENTIAL" "1" "Nov 12, 2018" "2018.4" "GROMACS"
.SH NAME
gmx-potential \- Calculate the electrostatic potential across the box
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