Commit be53d79c authored by Nicholas Breen's avatar Nicholas Breen

New upstream version 2018.3

parent 8f966be4
...@@ -5,7 +5,7 @@ Installation guide ...@@ -5,7 +5,7 @@ Installation guide
Introduction to building GROMACS 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. want to check the up-to-date installation instructions.
...@@ -28,8 +28,8 @@ Quick and dirty installation ...@@ -28,8 +28,8 @@ Quick and dirty installation
Or, as a sequence of commands to execute: Or, as a sequence of commands to execute:
tar xfz gromacs-2018.2.tar.gz tar xfz gromacs-2018.3.tar.gz
cd gromacs-2018.2 cd gromacs-2018.3
mkdir build mkdir build
cd build cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
...@@ -153,7 +153,7 @@ offer competitive performance. We recommend against PGI because the ...@@ -153,7 +153,7 @@ offer competitive performance. We recommend against PGI because the
performance with C++ is very bad. performance with C++ is very bad.
The xlc compiler is not supported and has not been tested on POWER 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. instead, as it is being extensively tested.
You may also need the most recent version of other compiler toolchain 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 ...@@ -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 code you want to build. For example, download the source tarball and
use use
tar xfz gromacs-2018.2.tgz tar xfz gromacs-2018.3.tgz
cd gromacs-2018.2 cd gromacs-2018.3
mkdir build-gromacs mkdir build-gromacs
cd build-gromacs cd build-gromacs
cmake .. cmake ..
...@@ -994,7 +994,7 @@ The simplest way to run the checks is to build GROMACS with ...@@ -994,7 +994,7 @@ The simplest way to run the checks is to build GROMACS with
"-DREGRESSIONTEST_DOWNLOAD", and run "make check". GROMACS will "-DREGRESSIONTEST_DOWNLOAD", and run "make check". GROMACS will
automatically download and run the tests for you. Alternatively, you automatically download and run the tests for you. Alternatively, you
can download and unpack the GROMACS regression test suite 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 tarball yourself and use the advanced "cmake" option
"REGRESSIONTEST_PATH" to specify the path to the unpacked tarball, "REGRESSIONTEST_PATH" to specify the path to the unpacked tarball,
which will then be used for testing. If the above does not work, then which will then be used for testing. If the above does not work, then
......
...@@ -19,15 +19,15 @@ ...@@ -19,15 +19,15 @@
# Test oldest supported CUDA # Test oldest supported CUDA
# Test oldest supported Ubuntu # Test oldest supported Ubuntu
# Test MPI with CUDA # Test MPI with CUDA
# Test cmake version from before new FindCUDA support (in 3.8)
# Test MPMD PME with library MPI # Test MPMD PME with library MPI
# Test cmake FindCUDA functionality introduced in 3.8 gcc-4.8 gpu cuda-6.5 cmake-3.6.1 mpi npme=1 nranks=2 openmp
gcc-4.8 gpu cuda-6.5 cmake-3.8.1 mpi npme=1 nranks=2 openmp
# Test newest gcc supported by newest CUDA at time of release # Test newest gcc supported by newest CUDA at time of release
# Test thread-MPI with CUDA # 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 # 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 newest cmake at time of release
# Test with ThreadSanitizer (compiled without OpenMP, even though # Test with ThreadSanitizer (compiled without OpenMP, even though
......
...@@ -271,31 +271,6 @@ macro(gmx_gpu_setup) ...@@ -271,31 +271,6 @@ macro(gmx_gpu_setup)
if(NOT GMX_OPENMP) 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.") 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() 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 endif() # GMX_GPU
if (GMX_CLANG_CUDA) if (GMX_CLANG_CUDA)
...@@ -314,8 +289,12 @@ macro(gmx_gpu_setup) ...@@ -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) 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(_gmx_cuda_target_changed OR NOT GMX_GPU_DETECTION_DONE)
if((NOT GMX_CUDA_TARGET_SM AND NOT GMX_CUDA_TARGET_COMPUTE) OR # CUDA 9.0 does not support CC 2.0; if arch targets are
(GMX_CUDA_TARGET_SM MATCHES "2[01]" OR GMX_CUDA_TARGET_COMPUTE MATCHES "2[01]")) # 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.") 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) set_property(CACHE GMX_CUDA_NB_SINGLE_COMPILATION_UNIT PROPERTY VALUE ON)
else() else()
......
# #
# This file is part of the GROMACS molecular simulation package. # 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, # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the # and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org. # top-level source directory and at http://www.gromacs.org.
...@@ -35,22 +35,14 @@ ...@@ -35,22 +35,14 @@
# Manage CUDA nvcc compilation configuration, try to be smart to ease the users' # Manage CUDA nvcc compilation configuration, try to be smart to ease the users'
# pain as much as possible: # pain as much as possible:
# - use the CUDA_HOST_COMPILER if defined by the user, otherwise # - 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) # - check if nvcc works with CUDA_HOST_COMPILER and the generated nvcc and C++ flags
# - set icc compatibility mode to gcc 4.8.1 #
# - (advanced) variables set: # - (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 # * 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, # 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. # 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 # 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 # many projects, but which has a trivial workaround. It would be nicer
# to compile with nvcc and see that the workaround is necessary and # to compile with nvcc and see that the workaround is necessary and
...@@ -68,6 +60,8 @@ function(work_around_glibc_2_23) ...@@ -68,6 +60,8 @@ function(work_around_glibc_2_23)
endif() endif()
endfunction() endfunction()
gmx_check_if_changed(CUDA_HOST_COMPILER_CHANGED CUDA_HOST_COMPILER)
# set up host compiler and its options # set up host compiler and its options
if(CUDA_HOST_COMPILER_CHANGED) if(CUDA_HOST_COMPILER_CHANGED)
set(CUDA_HOST_COMPILER_OPTIONS "") set(CUDA_HOST_COMPILER_OPTIONS "")
...@@ -176,6 +170,32 @@ endif() ...@@ -176,6 +170,32 @@ endif()
# assemble the CUDA host compiler flags # assemble the CUDA host compiler flags
list(APPEND GMX_CUDA_NVCC_FLAGS "${CUDA_HOST_COMPILER_OPTIONS}") 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 # 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 # (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. # host compiler flags are already set.
......
...@@ -186,7 +186,7 @@ ...@@ -186,7 +186,7 @@
# The GROMACS convention is that these are the version number of the next # The GROMACS convention is that these are the version number of the next
# release that is going to be made from this branch. # release that is going to be made from this branch.
set(GMX_VERSION_MAJOR 2018) 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 # The suffix, on the other hand, is used mainly for betas and release
# candidates, where it signifies the most recent such release from # candidates, where it signifies the most recent such release from
# this branch; it will be empty before the first such release, as well # this branch; it will be empty before the first such release, as well
...@@ -203,7 +203,7 @@ set(GMX_VERSION_SUFFIX "") ...@@ -203,7 +203,7 @@ set(GMX_VERSION_SUFFIX "")
# code being able to dynamically link with a version of libgromacs # code being able to dynamically link with a version of libgromacs
# that might not work. # that might not work.
set(LIBRARY_SOVERSION_MAJOR 3) 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) set(LIBRARY_VERSION ${LIBRARY_SOVERSION_MAJOR}.${LIBRARY_SOVERSION_MINOR}.0)
##################################################################### #####################################################################
...@@ -231,7 +231,7 @@ set(REGRESSIONTEST_BRANCH "refs/heads/release-2018") ...@@ -231,7 +231,7 @@ set(REGRESSIONTEST_BRANCH "refs/heads/release-2018")
# build the regressiontests tarball with all the right naming. The # 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 # naming affects the md5sum that has to go here, and if it isn't right
# release workflow will report a failure. # 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 math(EXPR GMX_VERSION_NUMERIC
"${GMX_VERSION_MAJOR}*10000 + ${GMX_VERSION_PATCH}") "${GMX_VERSION_MAJOR}*10000 + ${GMX_VERSION_PATCH}")
......
...@@ -125,6 +125,7 @@ if (SPHINX_FOUND) ...@@ -125,6 +125,7 @@ if (SPHINX_FOUND)
fragments/doxygen-links.rst fragments/doxygen-links.rst
install-guide/index.rst install-guide/index.rst
release-notes/index.rst release-notes/index.rst
release-notes/2018/2018.3.rst
release-notes/2018/2018.2.rst release-notes/2018/2018.2.rst
release-notes/2018/2018.1.rst release-notes/2018/2018.1.rst
release-notes/2018/major/highlights.rst release-notes/2018/major/highlights.rst
......
.\" Man page generated from reStructuredText. .\" 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 .SH NAME
gmx-anadock \- Cluster structures from Autodock runs gmx-anadock \- Cluster structures from Autodock runs
. .
......
.\" Man page generated from reStructuredText. .\" 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 .SH NAME
gmx-anaeig \- Analyze eigenvectors/normal modes gmx-anaeig \- Analyze eigenvectors/normal modes
. .
......
.\" Man page generated from reStructuredText. .\" 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 .SH NAME
gmx-analyze \- Analyze data sets gmx-analyze \- Analyze data sets
. .
......
.\" Man page generated from reStructuredText. .\" 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 .SH NAME
gmx-angle \- Calculate distributions and correlations for angles and dihedrals gmx-angle \- Calculate distributions and correlations for angles and dihedrals
. .
......
.\" Man page generated from reStructuredText. .\" 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 .SH NAME
gmx-awh \- Extract data from an accelerated weight histogram (AWH) run gmx-awh \- Extract data from an accelerated weight histogram (AWH) run
. .
......
.\" Man page generated from reStructuredText. .\" 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 .SH NAME
gmx-bar \- Calculate free energy difference estimates through Bennett's acceptance ratio gmx-bar \- Calculate free energy difference estimates through Bennett's acceptance ratio
. .
......
.\" Man page generated from reStructuredText. .\" 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 .SH NAME
gmx-bundle \- Analyze bundles of axes, e.g., helices gmx-bundle \- Analyze bundles of axes, e.g., helices
. .
......
.\" Man page generated from reStructuredText. .\" 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 .SH NAME
gmx-check \- Check and compare files gmx-check \- Check and compare files
. .
......
.\" Man page generated from reStructuredText. .\" 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 .SH NAME
gmx-chi \- Calculate everything you want to know about chi and other dihedrals gmx-chi \- Calculate everything you want to know about chi and other dihedrals
. .
......
.\" Man page generated from reStructuredText. .\" 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 .SH NAME
gmx-cluster \- Cluster structures gmx-cluster \- Cluster structures
. .
......
.\" Man page generated from reStructuredText. .\" 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 .SH NAME
gmx-clustsize \- Calculate size distributions of atomic clusters gmx-clustsize \- Calculate size distributions of atomic clusters
. .
......
.\" Man page generated from reStructuredText. .\" 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 .SH NAME
gmx-confrms \- Fit two structures and calculates the RMSD gmx-confrms \- Fit two structures and calculates the RMSD
. .
......
.\" Man page generated from reStructuredText. .\" 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 .SH NAME
gmx-convert-tpr \- Make a modifed run-input file gmx-convert-tpr \- Make a modifed run-input file
. .
......
.\" Man page generated from reStructuredText. .\" 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 .SH NAME
gmx-covar \- Calculate and diagonalize the covariance matrix gmx-covar \- Calculate and diagonalize the covariance matrix
. .
......
.\" Man page generated from reStructuredText. .\" 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 .SH NAME
gmx-current \- Calculate dielectric constants and current autocorrelation function gmx-current \- Calculate dielectric constants and current autocorrelation function
. .
......
.\" Man page generated from reStructuredText. .\" 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 .SH NAME
gmx-density \- Calculate the density of the system gmx-density \- Calculate the density of the system
. .
......
.\" Man page generated from reStructuredText. .\" 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 .SH NAME
gmx-densmap \- Calculate 2D planar or axial-radial density maps gmx-densmap \- Calculate 2D planar or axial-radial density maps
. .
......
.\" Man page generated from reStructuredText. .\" 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 .SH NAME
gmx-densorder \- Calculate surface fluctuations gmx-densorder \- Calculate surface fluctuations
. .
......
.\" Man page generated from reStructuredText. .\" 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 .SH NAME
gmx-dielectric \- Calculate frequency dependent dielectric constants gmx-dielectric \- Calculate frequency dependent dielectric constants
. .
......
.\" Man page generated from reStructuredText. .\" 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 .SH NAME
gmx-dipoles \- Compute the total dipole plus fluctuations gmx-dipoles \- Compute the total dipole plus fluctuations
. .
......
.\" Man page generated from reStructuredText. .\" 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 .SH NAME
gmx-disre \- Analyze distance restraints gmx-disre \- Analyze distance restraints
. .
......
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.TH "GMX-DISTANCE" "1" "Jun 14, 2018" "2018.2" "GROMACS" .TH "GMX-DISTANCE" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME .SH NAME
gmx-distance \- Calculate distances between pairs of positions gmx-distance \- Calculate distances between pairs of positions
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.TH "GMX-DO_DSSP" "1" "Jun 14, 2018" "2018.2" "GROMACS" .TH "GMX-DO_DSSP" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME .SH NAME
gmx-do_dssp \- Assign secondary structure and calculate solvent accessible surface area gmx-do_dssp \- Assign secondary structure and calculate solvent accessible surface area
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.TH "GMX-DOS" "1" "Jun 14, 2018" "2018.2" "GROMACS" .TH "GMX-DOS" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME .SH NAME
gmx-dos \- Analyze density of states and properties based on that gmx-dos \- Analyze density of states and properties based on that
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.TH "GMX-DUMP" "1" "Jun 14, 2018" "2018.2" "GROMACS" .TH "GMX-DUMP" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME .SH NAME
gmx-dump \- Make binary files human readable gmx-dump \- Make binary files human readable
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.TH "GMX-DYECOUPL" "1" "Jun 14, 2018" "2018.2" "GROMACS" .TH "GMX-DYECOUPL" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME .SH NAME
gmx-dyecoupl \- Extract dye dynamics from trajectories gmx-dyecoupl \- Extract dye dynamics from trajectories
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.TH "GMX-DYNDOM" "1" "Jun 14, 2018" "2018.2" "GROMACS" .TH "GMX-DYNDOM" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME .SH NAME
gmx-dyndom \- Interpolate and extrapolate structure rotations gmx-dyndom \- Interpolate and extrapolate structure rotations
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.TH "GMX-EDITCONF" "1" "Jun 14, 2018" "2018.2" "GROMACS" .TH "GMX-EDITCONF" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME .SH NAME
gmx-editconf \- Convert and manipulates structure files gmx-editconf \- Convert and manipulates structure files
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.TH "GMX-ENECONV" "1" "Jun 14, 2018" "2018.2" "GROMACS" .TH "GMX-ENECONV" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME .SH NAME
gmx-eneconv \- Convert energy files gmx-eneconv \- Convert energy files
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.TH "GMX-ENEMAT" "1" "Jun 14, 2018" "2018.2" "GROMACS" .TH "GMX-ENEMAT" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME .SH NAME
gmx-enemat \- Extract an energy matrix from an energy file gmx-enemat \- Extract an energy matrix from an energy file
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.TH "GMX-ENERGY" "1" "Jun 14, 2018" "2018.2" "GROMACS" .TH "GMX-ENERGY" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME .SH NAME
gmx-energy \- Writes energies to xvg files and display averages gmx-energy \- Writes energies to xvg files and display averages
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.TH "GMX-FILTER" "1" "Jun 14, 2018" "2018.2" "GROMACS" .TH "GMX-FILTER" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME .SH NAME
gmx-filter \- Frequency filter trajectories, useful for making smooth movies gmx-filter \- Frequency filter trajectories, useful for making smooth movies
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.TH "GMX-FREEVOLUME" "1" "Jun 14, 2018" "2018.2" "GROMACS" .TH "GMX-FREEVOLUME" "1" "Aug 23, 2018" "2018.3" "GROMACS"
.SH NAME .SH NAME
gmx-freevolume \- Calculate free volume gmx-freevolume \- Calculate free volume
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