Commit e72142e2 authored by Nicholas Breen's avatar Nicholas Breen

Update upstream source from tag 'upstream/2018.3'

Update to upstream version '2018.3'
with Debian dir 5e249b19f2643c281b994a9a2e7f6c857c6a06c0
parents 017271ef be53d79c
......@@ -5,7 +5,7 @@ Installation guide
Introduction to building GROMACS
================================
These instructions pertain to building GROMACS 2018.2. You might also
These instructions pertain to building GROMACS 2018.3. 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-2018.2.tar.gz
cd gromacs-2018.2
tar xfz gromacs-2018.3.tar.gz
cd gromacs-2018.3
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 has not been tested on POWER
architectures for GROMACS-2018.2. We recommend to use the gcc compiler
architectures for GROMACS-2018.3. 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
......@@ -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-2018.2.tgz
cd gromacs-2018.2
tar xfz gromacs-2018.3.tgz
cd gromacs-2018.3
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-2018.2.tar.gz
http://gerrit.gromacs.org/download/regressiontests-2018.3.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
......
......@@ -19,15 +19,15 @@
# Test oldest supported CUDA
# Test oldest supported Ubuntu
# Test MPI with CUDA
# Test cmake version from before new FindCUDA support (in 3.8)
# Test MPMD PME with library MPI
# Test cmake FindCUDA functionality introduced in 3.8
gcc-4.8 gpu cuda-6.5 cmake-3.8.1 mpi npme=1 nranks=2 openmp
gcc-4.8 gpu cuda-6.5 cmake-3.6.1 mpi npme=1 nranks=2 openmp
# Test newest gcc supported by newest CUDA at time of release
# Test thread-MPI with CUDA
# Test cmake version from before new FindCUDA support (in 3.8)
# Test cmake FindCUDA functionality introduced in 3.8
# Test SIMD implementation of pair search for GPU code-path
gcc-6 gpu cuda-9.0 thread-mpi openmp cmake-3.6.1 release-with-assert simd=avx2_256
gcc-6 gpu cuda-9.0 thread-mpi openmp cmake-3.8.1 release-with-assert simd=avx2_256
# Test newest cmake at time of release
# Test with ThreadSanitizer (compiled without OpenMP, even though
......
......@@ -271,31 +271,6 @@ macro(gmx_gpu_setup)
if(NOT GMX_OPENMP)
message(WARNING "To use GPU acceleration efficiently, mdrun requires OpenMP multi-threading. Without OpenMP a single CPU core can be used with a GPU which is not optimal. Note that with MPI multiple processes can be forced to use a single GPU, but this is typically inefficient. You need to set both C and C++ compilers that support OpenMP (CC and CXX environment variables, respectively) when using GPUs.")
endif()
if(NOT GMX_CLANG_CUDA)
gmx_check_if_changed(GMX_CHECK_NVCC CUDA_NVCC_EXECUTABLE CUDA_HOST_COMPILER CUDA_NVCC_FLAGS)
if(GMX_CHECK_NVCC OR NOT GMX_NVCC_WORKS)
message(STATUS "Check for working NVCC/C compiler combination")
execute_process(COMMAND ${CUDA_NVCC_EXECUTABLE} -ccbin ${CUDA_HOST_COMPILER} -c ${CUDA_NVCC_FLAGS} ${CMAKE_SOURCE_DIR}/cmake/TestCUDA.cu
RESULT_VARIABLE _cuda_test_res
OUTPUT_VARIABLE _cuda_test_out
ERROR_VARIABLE _cuda_test_err
OUTPUT_STRIP_TRAILING_WHITESPACE)
if(${_cuda_test_res})
message(STATUS "Check for working NVCC/C compiler combination - broken")
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()
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")
set(GMX_NVCC_WORKS TRUE CACHE INTERNAL "Nvcc can compile a trivial test program")
endif()
endif() # GMX_CHECK_NVCC
endif() #GMX_CLANG_CUDA
endif() # GMX_GPU
if (GMX_CLANG_CUDA)
......@@ -314,8 +289,12 @@ macro(gmx_gpu_setup)
gmx_check_if_changed(_gmx_cuda_target_changed GMX_CUDA_TARGET_SM GMX_CUDA_TARGET_COMPUTE CUDA_NVCC_FLAGS)
if(_gmx_cuda_target_changed OR NOT GMX_GPU_DETECTION_DONE)
if((NOT GMX_CUDA_TARGET_SM AND NOT GMX_CUDA_TARGET_COMPUTE) OR
(GMX_CUDA_TARGET_SM MATCHES "2[01]" OR GMX_CUDA_TARGET_COMPUTE MATCHES "2[01]"))
# CUDA 9.0 does not support CC 2.0; if arch targets are
# generated from a manually provided list, we check for 2x
# targets to see if single compilation unit needs to be on.
if((CUDA_VERSION VERSION_LESS "9.0") AND
((NOT GMX_CUDA_TARGET_SM AND NOT GMX_CUDA_TARGET_COMPUTE) OR
(GMX_CUDA_TARGET_SM MATCHES "2[01]" OR GMX_CUDA_TARGET_COMPUTE MATCHES "2[01]")))
message(STATUS "Enabling single compilation unit for the CUDA non-bonded module. Multiple compilation units are not compatible with CC 2.x devices, to enable the feature specify only CC >=3.0 target architectures in GMX_CUDA_TARGET_SM/GMX_CUDA_TARGET_COMPUTE.")
set_property(CACHE GMX_CUDA_NB_SINGLE_COMPILATION_UNIT PROPERTY VALUE ON)
else()
......
#
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
# Copyright (c) 2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
......@@ -35,22 +35,14 @@
# Manage CUDA nvcc compilation configuration, try to be smart to ease the users'
# pain as much as possible:
# - use the CUDA_HOST_COMPILER if defined by the user, otherwise
# - auto-detect compatible nvcc host compiler and set nvcc -ccbin (if not MPI wrapper)
# - set icc compatibility mode to gcc 4.8.1
# - check if nvcc works with CUDA_HOST_COMPILER and the generated nvcc and C++ flags
#
# - (advanced) variables set:
# * CUDA_HOST_COMPILER - the host compiler for nvcc (only with cmake <2.8.10)
# * CUDA_HOST_COMPILER_OPTIONS - the full host-compiler related option list passed to nvcc
#
# Note that from CMake 2.8.10 FindCUDA defines CUDA_HOST_COMPILER internally,
# so we won't set it ourselves, but hope that the module does a good job.
gmx_check_if_changed(CUDA_HOST_COMPILER_CHANGED CUDA_HOST_COMPILER)
# CUDA_HOST_COMPILER changed hence it is not auto-set anymore
if (CUDA_HOST_COMPILER_CHANGED AND CUDA_HOST_COMPILER_AUTOSET)
unset(CUDA_HOST_COMPILER_AUTOSET CACHE)
endif()
# glibc 2.23 changed string.h in a way that breaks CUDA compilation in
# many projects, but which has a trivial workaround. It would be nicer
# to compile with nvcc and see that the workaround is necessary and
......@@ -68,6 +60,8 @@ function(work_around_glibc_2_23)
endif()
endfunction()
gmx_check_if_changed(CUDA_HOST_COMPILER_CHANGED CUDA_HOST_COMPILER)
# set up host compiler and its options
if(CUDA_HOST_COMPILER_CHANGED)
set(CUDA_HOST_COMPILER_OPTIONS "")
......@@ -176,6 +170,32 @@ endif()
# assemble the CUDA host compiler flags
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)
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}} ${CMAKE_SOURCE_DIR}/cmake/TestCUDA.cu
RESULT_VARIABLE _cuda_test_res
OUTPUT_VARIABLE _cuda_test_out
ERROR_VARIABLE _cuda_test_err
OUTPUT_STRIP_TRAILING_WHITESPACE)
if(${_cuda_test_res})
message(${_cuda_test_err})
message(STATUS "Check for working NVCC/C compiler combination - broken")
if(${_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()
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")
set(GMX_NVCC_WORKS TRUE CACHE INTERNAL "Nvcc can compile a trivial test program")
endif()
endif() # GMX_CHECK_NVCC
# The flags are set as local variables which shadow the cache variables. The cache variables
# (can be set by the user) are appended. This is done in a macro to set the flags when all
# host compiler flags are already set.
......
......@@ -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 2)
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
......@@ -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 2)
set(LIBRARY_SOVERSION_MINOR 3)
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 "135149af467a37714a92bc29801cafda" CACHE INTERNAL "MD5 sum of the regressiontests tarball for this GROMACS version")
set(REGRESSIONTEST_MD5SUM "368aabf0eb4e6fbc9abb7961475f66de" 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/2018/2018.3.rst
release-notes/2018/2018.2.rst
release-notes/2018/2018.1.rst
release-notes/2018/major/highlights.rst
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANADOCK" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-ANADOCK" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-anadock \- Cluster structures from Autodock runs
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANAEIG" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-ANAEIG" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-anaeig \- Analyze eigenvectors/normal modes
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANALYZE" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-ANALYZE" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-analyze \- Analyze data sets
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANGLE" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-ANGLE" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-angle \- Calculate distributions and correlations for angles and dihedrals
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-AWH" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-AWH" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-awh \- Extract data from an accelerated weight histogram (AWH) run
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-BAR" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-BAR" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-bar \- Calculate free energy difference estimates through Bennett's acceptance ratio
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-BUNDLE" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-BUNDLE" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-bundle \- Analyze bundles of axes, e.g., helices
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CHECK" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-CHECK" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-check \- Check and compare files
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CHI" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-CHI" "1" "Aug 23, 2018" "2018.3" "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" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-CLUSTER" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-cluster \- Cluster structures
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CLUSTSIZE" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-CLUSTSIZE" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-clustsize \- Calculate size distributions of atomic clusters
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CONFRMS" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-CONFRMS" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-confrms \- Fit two structures and calculates the RMSD
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CONVERT-TPR" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-CONVERT-TPR" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-convert-tpr \- Make a modifed run-input file
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-COVAR" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-COVAR" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-covar \- Calculate and diagonalize the covariance matrix
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CURRENT" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-CURRENT" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-current \- Calculate dielectric constants and current autocorrelation function
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DENSITY" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-DENSITY" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-density \- Calculate the density of the system
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DENSMAP" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-DENSMAP" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-densmap \- Calculate 2D planar or axial-radial density maps
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DENSORDER" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-DENSORDER" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-densorder \- Calculate surface fluctuations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DIELECTRIC" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-DIELECTRIC" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-dielectric \- Calculate frequency dependent dielectric constants
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DIPOLES" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-DIPOLES" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-dipoles \- Compute the total dipole plus fluctuations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DISRE" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-DISRE" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-disre \- Analyze distance restraints
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DISTANCE" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-DISTANCE" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-distance \- Calculate distances between pairs of positions
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DO_DSSP" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-DO_DSSP" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-do_dssp \- Assign secondary structure and calculate solvent accessible surface area
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DOS" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-DOS" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-dos \- Analyze density of states and properties based on that
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DUMP" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-DUMP" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-dump \- Make binary files human readable
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DYECOUPL" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-DYECOUPL" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-dyecoupl \- Extract dye dynamics from trajectories
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DYNDOM" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-DYNDOM" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-dyndom \- Interpolate and extrapolate structure rotations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-EDITCONF" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-EDITCONF" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-editconf \- Convert and manipulates structure files
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ENECONV" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-ENECONV" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-eneconv \- Convert energy files
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ENEMAT" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-ENEMAT" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-enemat \- Extract an energy matrix from an energy file
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ENERGY" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-ENERGY" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-energy \- Writes energies to xvg files and display averages
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-FILTER" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-FILTER" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-filter \- Frequency filter trajectories, useful for making smooth movies
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-FREEVOLUME" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-FREEVOLUME" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-freevolume \- Calculate free volume
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-GANGLE" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-GANGLE" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-gangle \- Calculate angles
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-GENCONF" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-GENCONF" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-genconf \- Multiply a conformation in 'random' orientations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-GENION" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-GENION" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-genion \- Generate monoatomic ions on energetically favorable positions
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-GENRESTR" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-GENRESTR" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-genrestr \- Generate position restraints or distance restraints for index groups
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-GROMPP" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-GROMPP" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-grompp \- Make a run input file
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-GYRATE" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-GYRATE" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-gyrate \- Calculate the radius of gyration
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-H2ORDER" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-H2ORDER" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-h2order \- Compute the orientation of water molecules
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-HBOND" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-HBOND" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-hbond \- Compute and analyze hydrogen bonds
.
......
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.TH "GMX-HELIX" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-HELIX" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-helix \- Calculate basic properties of alpha helices
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.TH "GMX-HELIXORIENT" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-HELIXORIENT" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-helixorient \- Calculate local pitch/bending/rotation/orientation inside helices
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.TH "GMX-HELP" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-HELP" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-help \- Print help information
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.TH "GMX-HYDORDER" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-HYDORDER" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-hydorder \- Compute tetrahedrality parameters around a given atom
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.TH "GMX-INSERT-MOLECULES" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-INSERT-MOLECULES" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-insert-molecules \- Insert molecules into existing vacancies
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.TH "GMX-LIE" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-LIE" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-lie \- Estimate free energy from linear combinations
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.TH "GMX-MAKE_EDI" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-MAKE_EDI" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-make_edi \- Generate input files for essential dynamics sampling
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.TH "GMX-MAKE_NDX" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-MAKE_NDX" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-make_ndx \- Make index files
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.TH "GMX-MDMAT" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-MDMAT" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-mdmat \- Calculate residue contact maps
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.TH "GMX-MDRUN" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-MDRUN" "1" "Aug 23, 2018" "2018.3" "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" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-MINDIST" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-mindist \- Calculate the minimum distance between two groups
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.TH "GMX-MK_ANGNDX" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-MK_ANGNDX" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-mk_angndx \- Generate index files for 'gmx angle'
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.TH "GMX-MORPH" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-MORPH" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-morph \- Interpolate linearly between conformations
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.TH "GMX-MSD" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-MSD" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-msd \- Calculates mean square displacements
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.TH "GMX-NMEIG" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-NMEIG" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-nmeig \- Diagonalize the Hessian for normal mode analysis
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.TH "GMX-NMENS" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-NMENS" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME
gmx-nmens \- Generate an ensemble of structures from the normal modes
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.TH "GMX-NMR" "1" "Jun 14, 2018" "2018.2" "GROMACS"
.TH "GMX-NMR" "1" "Aug 23, 2018" "2018.3" "GROMACS"