Commit c35c2d46 authored by Nicholas Breen's avatar Nicholas Breen

Update upstream source from tag 'upstream/2019'

Update to upstream version '2019'
with Debian dir 645a05118972a369801d7231b7abf2b2b91db5a3
parents dbd7ecf0 1d065f26
......@@ -217,7 +217,9 @@ endif()
set(REQUIRED_CUDA_COMPUTE_CAPABILITY 3.0)
# OpenCL required version: 1.2 or newer
set(REQUIRED_OPENCL_MIN_VERSION 1.2)
set(REQUIRED_OPENCL_MIN_VERSION_MAJOR 1)
set(REQUIRED_OPENCL_MIN_VERSION_MINOR 2)
set(REQUIRED_OPENCL_MIN_VERSION ${REQUIRED_OPENCL_MIN_VERSION_MAJOR}.${REQUIRED_OPENCL_MIN_VERSION_MINOR})
if(NOT GMX_USE_OPENCL)
# CUDA detection is done only if GMX_USE_OPENCL is OFF.
......
......@@ -5,8 +5,8 @@ Installation guide
Introduction to building GROMACS
================================
These instructions pertain to building GROMACS 2019-rc1. You might
also want to check the up-to-date installation instructions.
These instructions pertain to building GROMACS 2019. You might also
want to check the up-to-date installation instructions.
Quick and dirty installation
......@@ -28,8 +28,8 @@ Quick and dirty installation
Or, as a sequence of commands to execute:
tar xfz gromacs-2019-rc1.tar.gz
cd gromacs-2019-rc1
tar xfz gromacs-2019.tar.gz
cd gromacs-2019
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-rc1. We recommend to use the gcc
POWER architectures for GROMACS-2019. 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
......@@ -437,8 +437,8 @@ 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-rc1.tgz
cd gromacs-2019-rc1
tar xfz gromacs-2019.tgz
cd gromacs-2019
mkdir build-gromacs
cd build-gromacs
cmake ..
......@@ -1041,11 +1041,10 @@ 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-rc1.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.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
......
......@@ -47,6 +47,7 @@ extra_options = {
'tng' : Option.bool,
'mkl': Option.simple,
'fftpack': Option.simple,
'buildfftw': Option.simple,
'double': Option.simple,
'thread-mpi': Option.bool,
'clang_cuda': Option.bool,
......@@ -122,6 +123,10 @@ def do_build(context):
cmake_opts['GMX_FFT_LIBRARY'] = 'mkl'
elif context.opts.fftpack:
cmake_opts['GMX_FFT_LIBRARY'] = 'fftpack'
elif context.opts.buildfftw:
cmake_opts['GMX_BUILD_OWN_FFTW'] = 'ON'
cmake_opts['GMX_BUILD_OWN_FFTW_URL'] = 'ftp://ftp.gromacs.org/misc/fftw-3.3.8.tar.gz'
cmake_opts['GMX_BUILD_OWN_FFTW_MD5'] = '8aac833c943d8e90d51b697b27d4384d'
if context.opts.mkl or context.opts.atlas or context.opts.armpl:
cmake_opts['GMX_EXTERNAL_BLAS'] = 'ON'
cmake_opts['GMX_EXTERNAL_LAPACK'] = 'ON'
......
......@@ -83,7 +83,7 @@ gcc-6 openmp gpuhw=nvidia opencl-1.2 clFFT-2.14 mpi simd=avx2_256
# Test external clFFT (for build speed)
# Test AVX_128_FMA SIMD
# Test newest gcc at time of release
gcc-8 openmp simd=avx2_256 gpuhw=amd opencl-1.2 clFFT-2.14
gcc-8 openmp simd=avx2_256 gpuhw=amd opencl-1.2 clFFT-2.14 buildfftw
# TODO
# Add OpenMP support to ASAN build (but libomp.so in clang-4 reports leaks, so might need a suitable build or suppression)
......
......@@ -79,6 +79,10 @@ else()
if (NOT CUDA_VERSION VERSION_LESS 9.0)
list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_70")
endif()
# Enable this when clang (8.0 ?) introduces sm_75 support
#if (NOT CUDA_VERSION VERSION_LESS 10.0)
# list(APPEND _CUDA_CLANG_GENCODE_FLAGS "--cuda-gpu-arch=sm_75")
#endif()
endif()
if (GMX_CUDA_TARGET_SM)
set_property(CACHE GMX_CUDA_TARGET_SM PROPERTY HELPSTRING "List of CUDA GPU architecture codes to compile for (without the sm_ prefix)")
......
......@@ -112,10 +112,12 @@ if(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
set(GMX_FFT_ARMPL_FFTW3 1)
set(FFT_STATUS_MESSAGE "Using external FFT library - ARM Performance Library (FFTW3 compatibility mode)")
else()
set(GMX_FFT_FFTW3 1)
set(FFT_STATUS_MESSAGE "Using external FFT library - FFTW3")
endif()
endif()
if (NOT GMX_FFT_ARMPL_FFTW3)
set(GMX_FFT_FFTW3 1)
endif()
set(FFT_LIBRARIES ${${FFTW}_LIBRARIES})
elseif(${GMX_FFT_LIBRARY} STREQUAL "MKL")
......
......@@ -142,8 +142,10 @@ else()
elseif(CUDA_VERSION VERSION_LESS "9.0")
list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_60,code=compute_60")
list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_61,code=compute_61")
else() # version >= 9.0
elseif(CUDA_VERSION VERSION_LESS "10.0")
list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_70,code=compute_70")
else() # version >= 10.0
list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_75,code=compute_75")
endif()
endif()
......
......@@ -201,7 +201,7 @@ set(GMX_VERSION_PATCH 0)
# candidates, where it signifies the most recent such release from
# this branch; it will be empty before the first such release, as well
# as after the final release is out.
set(GMX_VERSION_SUFFIX "-rc1")
set(GMX_VERSION_SUFFIX "")
# Conventionally with libtool, any ABI change must change the major
# version number, the minor version number should change if it's just
......@@ -241,7 +241,7 @@ set(REGRESSIONTEST_BRANCH "refs/heads/release-2019")
# build the regressiontests tarball with all the right naming. The
# naming affects the md5sum that has to go here, and if it isn't right
# release workflow will report a failure.
set(REGRESSIONTEST_MD5SUM "69da7f6a5bfcdb38b202eb9f9df69d01" CACHE INTERNAL "MD5 sum of the regressiontests tarball for this GROMACS version")
set(REGRESSIONTEST_MD5SUM "1271a74bfe91028b7f184866d5aee98e" CACHE INTERNAL "MD5 sum of the regressiontests tarball for this GROMACS version")
math(EXPR GMX_VERSION_NUMERIC
"${GMX_VERSION_MAJOR}*10000 + ${GMX_VERSION_PATCH}")
......@@ -258,8 +258,8 @@ 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 "" CACHE INTERNAL "reserved doi for GROMACS manual" FORCE)
set(GMX_SOURCE_DOI "" CACHE INTERNAL "reserved doi for GROMACS source code" FORCE)
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)
#####################################################################
# git version info management
......
......@@ -15,3 +15,11 @@ When using CUDA 7.0 in a ``Debug`` build, if the PME FFT task is offloaded
to a GPU, a floating point exception will abort the :ref:`mdrun <gmx mdrun>` execution.
The exception originates from the CUDA FFT (cuFFT) library.
To avoid this issue, we advise using a later CUDA version.
Issues with GPU timer with OpenCL
---------------------------------
When building using OpenCL in ``Debug`` mode, it can happen that the GPU timer state gets
corrupted, leading to an assertion failure during the :ref:`mdrun <gmx mdrun>`.
This seems to be related to the load of other, unrelated tasks on the GPU.
......@@ -180,6 +180,8 @@ For maximum performance you will need to examine how you will use
parallelism is an advantage for |Gromacs|, but support for this is
generally built into your compiler and detected automatically.
.. _gmx-gpu-support:
GPU support
~~~~~~~~~~~
......@@ -500,6 +502,8 @@ easier next time. You can also do this kind of thing with ``ccmake``,
but you should avoid this, because the options set with ``-D`` will not
be able to be changed interactively in that run of ``ccmake``.
.. _gmx-simd-support:
SIMD support
~~~~~~~~~~~~
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANADOCK" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-ANADOCK" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-anadock \- Cluster structures from Autodock runs
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANAEIG" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-ANAEIG" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-anaeig \- Analyze eigenvectors/normal modes
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANALYZE" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-ANALYZE" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-analyze \- Analyze data sets
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANGLE" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-ANGLE" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-angle \- Calculate distributions and correlations for angles and dihedrals
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-AWH" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-AWH" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-awh \- Extract data from an accelerated weight histogram (AWH) run
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-BAR" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-BAR" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-bar \- Calculate free energy difference estimates through Bennett's acceptance ratio
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-BUNDLE" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-BUNDLE" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-bundle \- Analyze bundles of axes, e.g., helices
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CHECK" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-CHECK" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-check \- Check and compare files
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CHI" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-CHI" "1" "Dec 31, 2018" "2019" "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" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-CLUSTER" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-cluster \- Cluster structures
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CLUSTSIZE" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-CLUSTSIZE" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-clustsize \- Calculate size distributions of atomic clusters
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CONFRMS" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-CONFRMS" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-confrms \- Fit two structures and calculates the RMSD
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CONVERT-TPR" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-CONVERT-TPR" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-convert-tpr \- Make a modifed run-input file
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-COVAR" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-COVAR" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-covar \- Calculate and diagonalize the covariance matrix
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CURRENT" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-CURRENT" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-current \- Calculate dielectric constants and current autocorrelation function
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DENSITY" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-DENSITY" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-density \- Calculate the density of the system
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DENSMAP" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-DENSMAP" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-densmap \- Calculate 2D planar or axial-radial density maps
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-DENSORDER" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-DENSORDER" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-densorder \- Calculate surface fluctuations
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-DIELECTRIC" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-DIELECTRIC" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-dielectric \- Calculate frequency dependent dielectric constants
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-DIPOLES" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-DIPOLES" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-dipoles \- Compute the total dipole plus fluctuations
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-DISRE" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-DISRE" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-disre \- Analyze distance restraints
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-DISTANCE" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-DISTANCE" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-distance \- Calculate distances between pairs of positions
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DO_DSSP" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-DO_DSSP" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-do_dssp \- Assign secondary structure and calculate solvent accessible surface area
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-DOS" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-DOS" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-dos \- Analyze density of states and properties based on that
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-DUMP" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-DUMP" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-dump \- Make binary files human readable
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-DYECOUPL" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-DYECOUPL" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-dyecoupl \- Extract dye dynamics from trajectories
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-DYNDOM" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-DYNDOM" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-dyndom \- Interpolate and extrapolate structure rotations
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-EDITCONF" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-EDITCONF" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-editconf \- Convert and manipulates structure files
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-ENECONV" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-ENECONV" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-eneconv \- Convert energy files
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-ENEMAT" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-ENEMAT" "1" "Dec 31, 2018" "2019" "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" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-ENERGY" "1" "Dec 31, 2018" "2019" "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" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-FILTER" "1" "Dec 31, 2018" "2019" "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" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-FREEVOLUME" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-freevolume \- Calculate free volume
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-GANGLE" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-GANGLE" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-gangle \- Calculate angles
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-GENCONF" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-GENCONF" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-genconf \- Multiply a conformation in 'random' orientations
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-GENION" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-GENION" "1" "Dec 31, 2018" "2019" "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" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-GENRESTR" "1" "Dec 31, 2018" "2019" "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" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-GROMPP" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-grompp \- Make a run input file
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-GYRATE" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-GYRATE" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-gyrate \- Calculate the radius of gyration
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-H2ORDER" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-H2ORDER" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-h2order \- Compute the orientation of water molecules
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-HBOND" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-HBOND" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-hbond \- Compute and analyze hydrogen bonds
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-HELIX" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-HELIX" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-helix \- Calculate basic properties of alpha helices
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-HELIXORIENT" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-HELIXORIENT" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-helixorient \- Calculate local pitch/bending/rotation/orientation inside helices
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-HELP" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-HELP" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-help \- Print help information
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-HYDORDER" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-HYDORDER" "1" "Dec 31, 2018" "2019" "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" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-INSERT-MOLECULES" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-insert-molecules \- Insert molecules into existing vacancies
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-LIE" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-LIE" "1" "Dec 31, 2018" "2019" "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" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-MAKE_EDI" "1" "Dec 31, 2018" "2019" "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" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-MAKE_NDX" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-make_ndx \- Make index files
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-MDMAT" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-MDMAT" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-mdmat \- Calculate residue contact maps
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.TH "GMX-MDRUN" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-MDRUN" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-mdrun \- Perform a simulation, do a normal mode analysis or an energy minimization
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.TH "GMX-MINDIST" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-MINDIST" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-mindist \- Calculate the minimum distance between two groups
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.TH "GMX-MK_ANGNDX" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-MK_ANGNDX" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-mk_angndx \- Generate index files for 'gmx angle'
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.TH "GMX-MORPH" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-MORPH" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-morph \- Interpolate linearly between conformations
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.TH "GMX-MSD" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-MSD" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-msd \- Calculates mean square displacements
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.TH "GMX-NMEIG" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-NMEIG" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-nmeig \- Diagonalize the Hessian for normal mode analysis
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.TH "GMX-NMENS" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-NMENS" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-nmens \- Generate an ensemble of structures from the normal modes
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.TH "GMX-NMR" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-NMR" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-nmr \- Analyze nuclear magnetic resonance properties from an energy file
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.TH "GMX-NMTRAJ" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-NMTRAJ" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-nmtraj \- Generate a virtual oscillating trajectory from an eigenvector
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.TH "GMX-ORDER" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-ORDER" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-order \- Compute the order parameter per atom for carbon tails
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.TH "GMX-PAIRDIST" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.TH "GMX-PAIRDIST" "1" "Dec 31, 2018" "2019" "GROMACS"
.SH NAME
gmx-pairdist \- Calculate pairwise distances between groups of positions
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