...
 
Commits (2)
......@@ -5,7 +5,7 @@ Installation guide
Introduction to building GROMACS
================================
These instructions pertain to building GROMACS 2019-beta3. You might
These instructions pertain to building GROMACS 2019-rc1. You might
also want to check the up-to-date installation instructions.
......@@ -28,8 +28,8 @@ Quick and dirty installation
Or, as a sequence of commands to execute:
tar xfz gromacs-2019-beta3.tar.gz
cd gromacs-2019-beta3
tar xfz gromacs-2019-rc1.tar.gz
cd gromacs-2019-rc1
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
......@@ -107,19 +107,6 @@ of "xxx" :
* "-DCMAKE_BUILD_TYPE=Debug" to build GROMACS in debug mode
Building with MiMiC QM/MM support
---------------------------------
MiMiC QM/MM interface integration will require linking against MiMiC
communication library, that establishes the communication channel
between GROMACS and CPMD. Check that the installation folder of the
library is added to CMAKE_PREFIX_PATH if it is installed in non-
standard location. Building QM/MM-capable version requires double-
precision version of GROMACS compiled with MPI support:
* "-DGMX_DOUBLE=ON -DGMX_MPI -DGMX_MIMIC=ON"
Building older versions
-----------------------
......@@ -165,8 +152,8 @@ Other compilers may work (Cray, Pathscale, older clang) but do not
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-2019-beta3. We recommend to use the gcc
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
compiler instead, as it is being extensively tested.
You may also need the most recent version of other compiler toolchain
......@@ -364,6 +351,22 @@ The full list and order(!) of libraries you require are found in
Intel’s MKL documentation for your system.
Using ARM Performance Libraries
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The ARM Performance Libraries provides FFT transforms implementation
for ARM architectures. Preliminary support is provided for ARMPL in
GROMACS through its FFTW-compatible API. Assuming that the ARM HPC
toolchain environment including the ARMPL paths are set up (e.g.
through loading the appropriate modules like "module load Module-
Prefix/arm-hpc-compiler-X.Y/armpl/X.Y") use the following cmake
options:
cmake -DGMX_FFT_LIBRARY=fftw3 \
-DFFTWF_LIBRARY="${ARMPL_DIR}/lib/libarmpl_lp64.so" \
-DFFTWF_INCLUDE_DIR=${ARMPL_DIR}/include
Other optional build components
-------------------------------
......@@ -434,8 +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-beta3.tgz
cd gromacs-2019-beta3
tar xfz gromacs-2019-rc1.tgz
cd gromacs-2019-rc1
mkdir build-gromacs
cd build-gromacs
cmake ..
......@@ -594,7 +597,7 @@ to performance loss, e.g. on Intel Skylake-X/SP and AMD Zen.
11. "IBM_VMX" Power6 and similar Altivec processors have this.
12. "IBM_VSX" Power7, Power8 and later have this.
12. "IBM_VSX" Power7, Power8, Power9 and later have this.
13. "ARM_NEON" 32-bit ARMv7 with NEON support.
......@@ -856,8 +859,9 @@ otherwise fall back on a version of BLAS internal to GROMACS. The
internal versions are fine for normal use. If you need to specify a
non-standard path to search, use
"-DCMAKE_PREFIX_PATH=/path/to/search". If you need to specify a
library with a non-standard name (e.g. ESSL on Power machines), then
set "-DGMX_BLAS_USER=/path/to/reach/lib/libwhatever.a".
library with a non-standard name (e.g. ESSL on Power machines or ARMPL
on ARM machines), then set
"-DGMX_BLAS_USER=/path/to/reach/lib/libwhatever.a".
If you are using Intel MKL for FFT, then the BLAS and LAPACK it
provides are used automatically. This could be over-ridden with
......@@ -868,6 +872,21 @@ will be automatically used for BLAS and LAPACK. This could be over-
ridden with "GMX_BLAS_USER", etc.
Building with MiMiC QM/MM support
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MiMiC QM/MM interface integration will require linking against MiMiC
communication library, that establishes the communication channel
between GROMACS and CPMD. The MiMiC Communication library can be
downloaded here. Compile and install it. Check that the installation
folder of the MiMiC library is added to CMAKE_PREFIX_PATH if it is
installed in non-standard location. Building QM/MM-capable version
requires double-precision version of GROMACS compiled with MPI
support:
* "-DGMX_DOUBLE=ON -DGMX_MPI -DGMX_MIMIC=ON"
Changing the names of GROMACS binaries and libraries
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......@@ -1022,7 +1041,7 @@ The simplest way to run the checks is to build GROMACS with
"-DREGRESSIONTEST_DOWNLOAD", and run "make check". GROMACS will
automatically download and run the tests for you. Alternatively, you
can download and unpack the GROMACS regression test suite
http://gerrit.gromacs.org/download/regressiontests-2019-beta3.tar.gz
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
......
......@@ -67,6 +67,9 @@ def do_build(context):
cmake_opts['CMAKE_BUILD_TYPE'] = 'Debug'
cmake_opts['GMX_USE_RDTSCP'] = 'DETECT'
if not context.opts.msvc and not context.opts.mdrun_only and not context.opts.static:
cmake_opts['GMXAPI'] = 'ON'
if context.opts.reference:
cmake_opts['CMAKE_BUILD_TYPE'] = 'Reference'
elif context.opts['release']:
......@@ -119,13 +122,19 @@ def do_build(context):
cmake_opts['GMX_FFT_LIBRARY'] = 'mkl'
elif context.opts.fftpack:
cmake_opts['GMX_FFT_LIBRARY'] = 'fftpack'
if context.opts.mkl or context.opts.atlas:
if context.opts.mkl or context.opts.atlas or context.opts.armpl:
cmake_opts['GMX_EXTERNAL_BLAS'] = 'ON'
cmake_opts['GMX_EXTERNAL_LAPACK'] = 'ON'
if context.opts.clFFT:
cmake_opts['GMX_EXTERNAL_CLFFT'] = 'ON'
cmake_opts['clFFT_ROOT'] = context.env.clFFT_root
if context.opts.armpl:
cmake_opts['FFTWF_LIBRARY'] = os.path.join(context.env.armpl_dir, 'lib/libarmpl_lp64.so')
cmake_opts['FFTWF_INCLUDE_DIR'] = os.path.join(context.env.armpl_dir, 'include')
cmake_opts['GMX_BLAS_USER'] = os.path.join(context.env.armpl_dir, 'lib/libarmpl_lp64.so')
cmake_opts['GMX_LAPACK_USER'] = os.path.join(context.env.armpl_dir, 'lib/libarmpl_lp64.so')
if context.opts.hwloc is False:
cmake_opts['GMX_HWLOC'] = 'OFF'
......
......@@ -67,7 +67,9 @@ icc-18 msvc-2017 fftpack simd=avx2_256 release
#gcc-7 armhpc-18.2 openmp simd=ARM_NEON_ASIMD release
# Test ARM HPC compier toolchain with armclang
armclang-18.4 armhpc-18.4 openmp simd=ARM_NEON_ASIMD release-with-assert
# Test ARMPL for FFTs
# Test linking against ARMPL for BLAS/LAPACK
armclang-18.4 armhpc-18.4 armpl openmp simd=ARM_NEON_ASIMD release-with-assert
# TODO
# Add SIMD + OpenMP + CUDA asan build
......
......@@ -101,11 +101,23 @@ if(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
set(FFT_WARNING_MESSAGE "The FFTW library was compiled with neither --enable-sse nor --enable-sse2; those would have enabled SSE(2) SIMD instructions. This will give suboptimal performance. You should (re)compile the FFTW library with --enable-sse2 and --enable-avx (and --enable-avx2 or --enable-avx512 if supported).")
endif()
endif()
set(FFT_STATUS_MESSAGE "Using external FFT library - FFTW3")
find_path(ARMPL_INCLUDE_DIR "armpl.h" HINTS ${${FFTW}_INCLUDE_DIRS}
NO_DEFAULT_PATH
NO_CMAKE_ENVIRONMENT_PATH
NO_CMAKE_PATH
NO_SYSTEM_ENVIRONMENT_PATH
NO_CMAKE_SYSTEM_PATH)
if (ARMPL_INCLUDE_DIR)
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()
set(FFT_LIBRARIES ${${FFTW}_LIBRARIES})
set(GMX_FFT_FFTW3 1)
elseif(${GMX_FFT_LIBRARY} STREQUAL "MKL")
# Intel 11 and up makes life somewhat easy if you just want to use
# all their stuff. It's not easy if you only want some of their
......
......@@ -71,7 +71,7 @@ function(gmx_manage_lmfit)
# we will not be installing any content.
install(TARGETS lmfit EXPORT libgromacs)
set(HAVE_LMFIT_VALUE TRUE)
set(HAVE_LMFIT 1 CACHE INTERNAL "Is lmfit found?")
elseif(GMX_USE_LMFIT STREQUAL "EXTERNAL")
# Find an external lmfit library.
find_package(Lmfit ${GMX_LMFIT_MINIMUM_REQUIRED_VERSION})
......@@ -79,7 +79,7 @@ function(gmx_manage_lmfit)
message(FATAL_ERROR "External lmfit could not be found, please adjust your pkg-config path to include the lmfit.pc file")
endif()
set(HAVE_LMFIT_VALUE TRUE)
set(HAVE_LMFIT 1 CACHE INTERNAL "Is lmfit found?")
else()
# Create a dummy link target so the calling code doesn't need to know
# whether lmfit support is being compiled.
......@@ -88,6 +88,6 @@ function(gmx_manage_lmfit)
# we will not be installing any content.
install(TARGETS lmfit EXPORT libgromacs)
set(HAVE_LMFIT_VALUE FALSE)
set(HAVE_LMFIT 0 CACHE INTERNAL "Is lmfit found?")
endif()
endfunction()
......@@ -62,10 +62,18 @@ macro(find_power_vsx_toolchain_flags TOOLCHAIN_C_FLAGS_VARIABLE TOOLCHAIN_CXX_FL
if(CPU_DETECTION_BRAND MATCHES "POWER7")
gmx_test_cflag(GNU_C_VSX_POWER7 "-mcpu=power7 -mtune=power7" ${TOOLCHAIN_C_FLAGS_VARIABLE})
gmx_test_cflag(GNU_CXX_VSX_POWER7 "-mcpu=power7 -mtune=power7" ${TOOLCHAIN_CXX_FLAGS_VARIABLE})
elseif(CPU_DETECTION_BRAND MATCHES "POWER8")
# Enable power8 vector extensions on such platforms.
gmx_test_cflag(GNU_C_VSX_POWER8 "-mcpu=power8 -mpower8-vector -mpower8-fusion" ${TOOLCHAIN_C_FLAGS_VARIABLE})
gmx_test_cflag(GNU_CXX_VSX_POWER8 "-mcpu=power8 -mpower8-vector -mpower8-fusion" ${TOOLCHAIN_CXX_FLAGS_VARIABLE})
elseif(CPU_DETECTION_BRAND MATCHES "POWER9")
# Enable power9 vector extensions on such platforms.
# TODO consider whether adding " -mpower9-vector -mpower9-fusion"
# is an advantage.
gmx_test_cflag(GNU_C_VSX_POWER9 "-mcpu=power9 -mtune=power9" ${TOOLCHAIN_C_FLAGS_VARIABLE})
gmx_test_cflag(GNU_CXX_VSX_POWER9 "-mcpu=power9 -mtune=power9" ${TOOLCHAIN_CXX_FLAGS_VARIABLE})
else()
# Enable power8 vector extensions on all platforms except old Power7.
gmx_test_cflag(GNU_C_VSX_POWER8 "-mcpu=power8 -mpower8-vector -mpower8-fusion -mdirect-move" ${TOOLCHAIN_C_FLAGS_VARIABLE})
gmx_test_cflag(GNU_CXX_VSX_POWER8 "-mcpu=power8 -mpower8-vector -mpower8-fusion -mdirect-move" ${TOOLCHAIN_CXX_FLAGS_VARIABLE})
# Don't add arch-specific flags for unknown architectures.
endif()
# Altivec was originally single-only, and it took a while for compilers
# to support the double-precision features in VSX.
......
......@@ -113,6 +113,14 @@ using myInt = int;
// Test template using statement
template<class T> using myPointer = T*;
myPointer<int> x;
// Test in-class array initalizers used with constructor initializer lists
struct TestStruct
{
float a[3][3] = {{0}}; // in-class initializer
float b; // not initialized until constructor initializer list
TestStruct();
};
TestStruct::TestStruct() : b(0) {}
int main() {
// Test nullptr
double *x = nullptr;
......@@ -146,6 +154,8 @@ int main() {
if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS "19.0.23026")
message(FATAL_ERROR "GROMACS requires version 2015 (19.0.23026) or later of the MSVC C++ compiler for complete C++11 support")
endif()
elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "XL")
message(FATAL_ERROR "No known version of xlC can compile the normal C++11 code in GROMACS, highest version checked is 16.1.0")
endif()
if(CXX11_SUPPORTED)
set(${CXX11_CXX_FLAG_NAME} ${CXX11_CXX_FLAG} PARENT_SCOPE)
......
......@@ -44,9 +44,9 @@
# if convert is working or not.
function(GMX_TEST_IMAGEMAGICK VARIABLE)
set(value_ OFF)
if(NOT ${ImageMagick_CONVERT_FOUND})
MESSAGE(STATUS "No image conversion possible without ImageMagick")
set(value_ OFF)
elseif(NOT DEFINED ${VARIABLE})
set(TEMPDIR "${CMAKE_CURRENT_BINARY_DIR}/imagemagicktmp")
FILE(MAKE_DIRECTORY ${TEMPDIR})
......@@ -58,13 +58,21 @@ function(GMX_TEST_IMAGEMAGICK VARIABLE)
OUTPUT_QUIET
ERROR_QUIET
)
FILE(REMOVE_RECURSE ${TEMPDIR})
if (${TEST_OUTPUT} EQUAL 0)
if (EXISTS ${SAMPLE_OUTPUT})
set(value_ ON)
else()
MESSAGE(STATUS "Could not convert sample image, ImageMagick convert can not be used")
if (GMX_BUILD_MANUAL)
set(type_ "WARNING")
else()
set(type_ "STATUS")
endif()
MESSAGE(${type_} "Could not convert sample image, ImageMagick convert can not be used")
set(value_ OFF)
endif()
FILE(REMOVE_RECURSE ${TEMPDIR})
endif()
if(NOT DEFINED ${VARIABLE})
set(${VARIABLE} ${value_} CACHE INTERNAL "Test if image conversion works")
mark_as_advanced(${VARIABLE})
endif()
set(${VARIABLE} ${value_} CACHE INTERNAL "Test if image conversion works")
mark_as_advanced(${VARIABLE})
endfunction()
......@@ -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 "-beta3")
set(GMX_VERSION_SUFFIX "-rc1")
# 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 "10279cbb59912e11959fdd3981ad9c6f" CACHE INTERNAL "MD5 sum of the regressiontests tarball for this GROMACS version")
set(REGRESSIONTEST_MD5SUM "69da7f6a5bfcdb38b202eb9f9df69d01" CACHE INTERNAL "MD5 sum of the regressiontests tarball for this GROMACS version")
math(EXPR GMX_VERSION_NUMERIC
"${GMX_VERSION_MAJOR}*10000 + ${GMX_VERSION_PATCH}")
......
......@@ -119,12 +119,13 @@ else()
elseif(NOT SPHINX_FOUND)
set(MANUAL_BUILD_IS_POSSIBLE OFF)
set(MANUAL_BUILD_NOT_POSSIBLE_REASON "Sphinx has not been found and is needed to create the LaTex input files")
elseif(NOT PDFLATEX_COMPILER OR NOT IMAGE_CONVERT_POSSIBLE)
elseif(NOT PDFLATEX_COMPILER)
set(MANUAL_BUILD_IS_POSSIBLE OFF)
set(MANUAL_BUILD_NOT_POSSIBLE_REASON "pdflatex or some other dependency (ImageMagick convert) is not available")
if (NOT IMAGE_CONVERT_POSSIBLE)
set(NO_IMAGE_CONVERT_REASON "Can not convert files for online or pdf manual")
endif()
set(MANUAL_BUILD_NOT_POSSIBLE_REASON "pdflatex is not available")
elseif(NOT IMAGE_CONVERT_POSSIBLE)
set(MANUAL_BUILD_IS_POSSIBLE OFF)
set(MANUAL_BUILD_NOT_POSSIBLE_REASON "a working form of ImageMagick convert is not available")
set(NO_IMAGE_CONVERT_REASON "Can not convert files for online or pdf manual")
# TODO Later, identify other dependencies like bibtex,
# make_index, date, some graphics conversion program,
# etc. Perhaps patch UseLATEX.cmake and contribute upstream.
......@@ -229,6 +230,7 @@ if (SPHINX_FOUND)
reference-manual/special/qmmm.rst
reference-manual/special/vmd-imd.rst
reference-manual/special/membrane-embedding.rst
reference-manual/special/mimic-qmmm.rst
# Analysis chapter
reference-manual/analysis.rst
reference-manual/analysis/using-groups.rst
......@@ -345,6 +347,7 @@ if (SPHINX_FOUND)
dev-manual/includestyle.rst
dev-manual/index.rst
dev-manual/jenkins.rst
dev-manual/known-issues.rst
dev-manual/language-features.rst
dev-manual/naming.rst
dev-manual/overview.rst
......
......@@ -289,6 +289,8 @@ latex_elements = {
'pointsize': '11',
# Additional stuff for the LaTeX preamble.
# The tocdepth setting is needed to overwrite the default value set by Sphinx
# to get a more detailed toctree in the pdf version of the manual.
'preamble': r'''
\usepackage{here}
\usepackage{picins}
......@@ -304,6 +306,7 @@ latex_elements = {
\usepackage{pdflscape}
\pagenumbering{roman}
\usepackage{array}
\setcounter{tocdepth}{2}
''',
# Format output to avoid empty pages
'classoptions': ',openany,oneside'
......
......@@ -58,6 +58,7 @@ locations in the developer guide.
documentation-generation
style
tools
known-issues
*********************
Doxygen documentation
......
.. _gmx-dev-known-issues:
Known issues relevant for developers
====================================
This is a non-exhaustive list of known issues that have been observed
and can be of interest for developers. These have not been solved
because they are either outside the scope of the GROMACS project
or are are simply too difficult or tedious to address ourselves.
FP exceptions with CUDA 7.0
---------------------------
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.
......@@ -12,23 +12,36 @@ Welcome to the |Gromacs| documentation!
The complete documentation is also available as a `printable PDF here`_.
.. toctree::
:maxdepth: 1
download
release-notes/index
install-guide/index
user-guide/index
how-to/index
reference-manual/index
dev-manual/index
==================
Indices and tables
==================
* :ref:`genindex`
.. toctree::
:maxdepth: 1
download
release-notes/index
install-guide/index
user-guide/index
how-to/index
reference-manual/index
dev-manual/index
==================
Indices and tables
==================
* :ref:`genindex`
.. only:: latex
The release notes can be found online at http://manual.gromacs.org/current/release-notes/index.html
.. toctree::
:maxdepth: 1
download
install-guide/index
user-guide/index
how-to/index
reference-manual/index
dev-manual/index
.. _printable PDF here: `gmx-manual`_
......
......@@ -83,18 +83,6 @@ appropriate value instead of ``xxx`` :
* ``-DGMX_FFT_LIBRARY=xxx`` to select whether to use ``fftw3``, ``mkl`` or ``fftpack`` libraries for `FFT support`_
* ``-DCMAKE_BUILD_TYPE=Debug`` to build |Gromacs| in debug mode
Building with MiMiC QM/MM support
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
MiMiC QM/MM interface integration will require linking against MiMiC
communication library, that establishes the communication channel between
|Gromacs| and CPMD. Check that the installation folder of the library
is added to CMAKE_PREFIX_PATH if it is installed in non-standard location.
Building QM/MM-capable version requires double-precision version of |Gromacs|
compiled with MPI support:
* ``-DGMX_DOUBLE=ON -DGMX_MPI -DGMX_MIMIC=ON``
Building older versions
^^^^^^^^^^^^^^^^^^^^^^^
......@@ -135,9 +123,9 @@ Other compilers may work (Cray, Pathscale, older clang) but do
not 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|\ -\ |version|. We recommend to use the gcc
compiler instead, as it is being extensively tested.
The xlc compiler is not supported and version 16.1 does not compile on
POWER architectures for |Gromacs|\ -\ |version|. 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
components beside the compiler itself (e.g. assembler or linker);
......@@ -334,6 +322,24 @@ If you need to customize this further, use
The full list and order(!) of libraries you require are found in Intel's MKL documentation for your system.
Using ARM Performance Libraries
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
The ARM Performance Libraries provides FFT transforms implementation for ARM
architectures.
Preliminary support is provided for ARMPL in |Gromacs| through its FFTW-compatible API.
Assuming that the ARM HPC toolchain environment including the ARMPL paths
are set up (e.g. through loading the appropriate modules like
``module load Module-Prefix/arm-hpc-compiler-X.Y/armpl/X.Y``) use the following cmake
options:
::
cmake -DGMX_FFT_LIBRARY=fftw3 \
-DFFTWF_LIBRARY="${ARMPL_DIR}/lib/libarmpl_lp64.so" \
-DFFTWF_INCLUDE_DIR=${ARMPL_DIR}/include
Other optional build components
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
......@@ -554,7 +560,7 @@ lead to performance loss, e.g. on Intel Skylake-X/SP and AMD Zen.
9. ``AVX_512_KNL`` Knights Landing Xeon Phi processors
10. ``Sparc64_HPC_ACE`` Fujitsu machines like the K computer have this.
11. ``IBM_VMX`` Power6 and similar Altivec processors have this.
12. ``IBM_VSX`` Power7, Power8 and later have this.
12. ``IBM_VSX`` Power7, Power8, Power9 and later have this.
13. ``ARM_NEON`` 32-bit ARMv7 with NEON support.
14. ``ARM_NEON_ASIMD`` 64-bit ARMv8 and later.
......@@ -821,7 +827,8 @@ is found, and otherwise fall back on a version of BLAS internal to
accordingly. The internal versions are fine for normal use. If you
need to specify a non-standard path to search, use
``-DCMAKE_PREFIX_PATH=/path/to/search``. If you need to specify a
library with a non-standard name (e.g. ESSL on Power machines), then
library with a non-standard name (e.g. ESSL on Power machines
or ARMPL on ARM machines), then
set ``-DGMX_BLAS_USER=/path/to/reach/lib/libwhatever.a``.
If you are using Intel MKL_ for FFT, then the BLAS and
......@@ -832,6 +839,22 @@ On Apple platforms where the Accelerate Framework is available, these
will be automatically used for BLAS and LAPACK. This could be
over-ridden with ``GMX_BLAS_USER``, etc.
.. _installing with MiMiC:
Building with MiMiC QM/MM support
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
MiMiC QM/MM interface integration will require linking against MiMiC
communication library, that establishes the communication channel
between |Gromacs| and CPMD. The MiMiC Communication library can be
downloaded `here <https://gitlab.com/MiMiC-projects/CommLib>`__.
Compile and install it. Check that the installation folder of the
MiMiC library is added to CMAKE_PREFIX_PATH if it is installed in
non-standard location. Building QM/MM-capable version requires
double-precision version of |Gromacs| compiled with MPI support:
* ``-DGMX_DOUBLE=ON -DGMX_MPI -DGMX_MIMIC=ON``
Changing the names of |Gromacs| binaries and libraries
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANADOCK" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-ANADOCK" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-anadock \- Cluster structures from Autodock runs
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANAEIG" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-ANAEIG" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-anaeig \- Analyze eigenvectors/normal modes
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANALYZE" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-ANALYZE" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-analyze \- Analyze data sets
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANGLE" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-ANGLE" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-angle \- Calculate distributions and correlations for angles and dihedrals
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-AWH" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-AWH" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-awh \- Extract data from an accelerated weight histogram (AWH) run
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-BAR" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-BAR" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-bar \- Calculate free energy difference estimates through Bennett's acceptance ratio
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-BUNDLE" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-BUNDLE" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-bundle \- Analyze bundles of axes, e.g., helices
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CHECK" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-CHECK" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-check \- Check and compare files
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CHI" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-CHI" "1" "Dec 14, 2018" "2019-rc1" "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" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-CLUSTER" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-cluster \- Cluster structures
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CLUSTSIZE" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-CLUSTSIZE" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-clustsize \- Calculate size distributions of atomic clusters
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CONFRMS" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-CONFRMS" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-confrms \- Fit two structures and calculates the RMSD
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CONVERT-TPR" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-CONVERT-TPR" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-convert-tpr \- Make a modifed run-input file
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-COVAR" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-COVAR" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-covar \- Calculate and diagonalize the covariance matrix
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CURRENT" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-CURRENT" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-current \- Calculate dielectric constants and current autocorrelation function
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DENSITY" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-DENSITY" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-density \- Calculate the density of the system
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DENSMAP" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-DENSMAP" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-densmap \- Calculate 2D planar or axial-radial density maps
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DENSORDER" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-DENSORDER" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-densorder \- Calculate surface fluctuations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DIELECTRIC" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-DIELECTRIC" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-dielectric \- Calculate frequency dependent dielectric constants
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DIPOLES" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-DIPOLES" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-dipoles \- Compute the total dipole plus fluctuations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DISRE" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-DISRE" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-disre \- Analyze distance restraints
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DISTANCE" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-DISTANCE" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-distance \- Calculate distances between pairs of positions
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DO_DSSP" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-DO_DSSP" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-do_dssp \- Assign secondary structure and calculate solvent accessible surface area
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DOS" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-DOS" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-dos \- Analyze density of states and properties based on that
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DUMP" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-DUMP" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-dump \- Make binary files human readable
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DYECOUPL" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-DYECOUPL" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-dyecoupl \- Extract dye dynamics from trajectories
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DYNDOM" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-DYNDOM" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-dyndom \- Interpolate and extrapolate structure rotations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-EDITCONF" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-EDITCONF" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-editconf \- Convert and manipulates structure files
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ENECONV" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-ENECONV" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-eneconv \- Convert energy files
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ENEMAT" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-ENEMAT" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-enemat \- Extract an energy matrix from an energy file
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ENERGY" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-ENERGY" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-energy \- Writes energies to xvg files and display averages
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-FILTER" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-FILTER" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-filter \- Frequency filter trajectories, useful for making smooth movies
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-FREEVOLUME" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-FREEVOLUME" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-freevolume \- Calculate free volume
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-GANGLE" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-GANGLE" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-gangle \- Calculate angles
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-GENCONF" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-GENCONF" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-genconf \- Multiply a conformation in 'random' orientations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-GENION" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-GENION" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-genion \- Generate monoatomic ions on energetically favorable positions
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-GENRESTR" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-GENRESTR" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-genrestr \- Generate position restraints or distance restraints for index groups
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-GROMPP" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-GROMPP" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-grompp \- Make a run input file
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-GYRATE" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-GYRATE" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-gyrate \- Calculate the radius of gyration
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-H2ORDER" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-H2ORDER" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-h2order \- Compute the orientation of water molecules
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-HBOND" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-HBOND" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-hbond \- Compute and analyze hydrogen bonds
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-HELIX" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-HELIX" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-helix \- Calculate basic properties of alpha helices
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-HELIXORIENT" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-HELIXORIENT" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-helixorient \- Calculate local pitch/bending/rotation/orientation inside helices
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-HELP" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-HELP" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-help \- Print help information
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-HYDORDER" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-HYDORDER" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-hydorder \- Compute tetrahedrality parameters around a given atom
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-INSERT-MOLECULES" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-INSERT-MOLECULES" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-insert-molecules \- Insert molecules into existing vacancies
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-LIE" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-LIE" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-lie \- Estimate free energy from linear combinations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-MAKE_EDI" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-MAKE_EDI" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-make_edi \- Generate input files for essential dynamics sampling
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-MAKE_NDX" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-MAKE_NDX" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-make_ndx \- Make index files
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-MDMAT" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-MDMAT" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-mdmat \- Calculate residue contact maps
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-MDRUN" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-MDRUN" "1" "Dec 14, 2018" "2019-rc1" "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" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-MINDIST" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-mindist \- Calculate the minimum distance between two groups
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-MK_ANGNDX" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-MK_ANGNDX" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-mk_angndx \- Generate index files for 'gmx angle'
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-MORPH" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-MORPH" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-morph \- Interpolate linearly between conformations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-MSD" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-MSD" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-msd \- Calculates mean square displacements
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-NMEIG" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-NMEIG" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-nmeig \- Diagonalize the Hessian for normal mode analysis
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-NMENS" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-NMENS" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-nmens \- Generate an ensemble of structures from the normal modes
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-NMR" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-NMR" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-nmr \- Analyze nuclear magnetic resonance properties from an energy file
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-NMTRAJ" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-NMTRAJ" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-nmtraj \- Generate a virtual oscillating trajectory from an eigenvector
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ORDER" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-ORDER" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-order \- Compute the order parameter per atom for carbon tails
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-PAIRDIST" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-PAIRDIST" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-pairdist \- Calculate pairwise distances between groups of positions
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-PDB2GMX" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-PDB2GMX" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-pdb2gmx \- Convert coordinate files to topology and FF-compliant coordinate files
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-PME_ERROR" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-PME_ERROR" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-pme_error \- Estimate the error of using PME with a given input file
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-POLYSTAT" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-POLYSTAT" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-polystat \- Calculate static properties of polymers
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-POTENTIAL" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-POTENTIAL" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-potential \- Calculate the electrostatic potential across the box
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-PRINCIPAL" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-PRINCIPAL" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-principal \- Calculate principal axes of inertia for a group of atoms
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-RAMA" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-RAMA" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-rama \- Compute Ramachandran plots
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-RDF" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-RDF" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-rdf \- Calculate radial distribution functions
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-REPORT-METHODS" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-REPORT-METHODS" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-report-methods \- Write short summary about the simulation setup to a text file and/or to the standard output.
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-RMS" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-RMS" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-rms \- Calculate RMSDs with a reference structure and RMSD matrices
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-RMSDIST" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-RMSDIST" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-rmsdist \- Calculate atom pair distances averaged with power -2, -3 or -6
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-RMSF" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-RMSF" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-rmsf \- Calculate atomic fluctuations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ROTACF" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-ROTACF" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-rotacf \- Calculate the rotational correlation function for molecules
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ROTMAT" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-ROTMAT" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-rotmat \- Plot the rotation matrix for fitting to a reference structure
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-SALTBR" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-SALTBR" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-saltbr \- Compute salt bridges
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-SANS" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-SANS" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-sans \- Compute small angle neutron scattering spectra
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-SASA" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-SASA" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-sasa \- Compute solvent accessible surface area
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-SAXS" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-SAXS" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-saxs \- Compute small angle X-ray scattering spectra
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-SELECT" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-SELECT" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-select \- Print general information about selections
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-SHAM" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-SHAM" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-sham \- Compute free energies or other histograms from histograms
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-SIGEPS" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-SIGEPS" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-sigeps \- Convert c6/12 or c6/cn combinations to and from sigma/epsilon
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-SOLVATE" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-SOLVATE" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-solvate \- Solvate a system
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.TH "GMX-SORIENT" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-SORIENT" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-sorient \- Analyze solvent orientation around solutes
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.TH "GMX-SPATIAL" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-SPATIAL" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-spatial \- Calculate the spatial distribution function
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.TH "GMX-SPOL" "1" "Nov 22, 2018" "2019-beta3" "GROMACS"
.TH "GMX-SPOL" "1" "Dec 14, 2018" "2019-rc1" "GROMACS"
.SH NAME
gmx-spol \- Analyze solvent dipole orientation and polarization around solutes
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