Commit fad1bbea authored by Nicholas Breen's avatar Nicholas Breen

Update upstream source from tag 'upstream/2018_beta3'

Update to upstream version '2018~beta3'
with Debian dir bd22974960941153775fe7615ffa1d4cd5bc2533
parents 73a2bacf fd6a0cf4
......@@ -5,7 +5,7 @@ Installation guide
Introduction to building GROMACS
================================
These instructions pertain to building GROMACS 2018-beta2. You might
These instructions pertain to building GROMACS 2018-beta3. 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-beta2.tar.gz
cd gromacs-2018-beta2
tar xfz gromacs-2018-beta3.tar.gz
cd gromacs-2018-beta3
mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
......@@ -149,7 +149,7 @@ 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-beta2. We recommend to use the gcc
architectures for GROMACS-2018-beta3. 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
......@@ -413,8 +413,8 @@ 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-beta2.tgz
cd gromacs-2018-beta2
tar xfz gromacs-2018-beta3.tgz
cd gromacs-2018-beta3
mkdir build-gromacs
cd build-gromacs
cmake ..
......@@ -968,7 +968,7 @@ 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-beta2.tar.gz
http://gerrit.gromacs.org/download/regressiontests-2018-beta3.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
......
......@@ -48,7 +48,8 @@ gcc-6 double x11
# Test double precision
# Test without OpenMP
# Test thread-MPI
clang-3.4 double thread-mpi no-openmp fftpack cmake-3.4.3
# Test AVX_128_FMA SIMD + Double (Important for Simd4N=Simd4 and sizeof(SimdInt32)!=4*GMX_SIMD_REAL_WIDTH)
clang-3.4 double simd=avx_128_fma thread-mpi no-openmp fftpack cmake-3.4.3
# Test newest clang at time of release
# Test with AddressSanitizer (without OpenMP, see below)
......
......@@ -32,6 +32,7 @@
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
include(gmxTestInlineASM)
include(gmxSimdFlags)
# gmx_detect_avx_512_fma_units()
......@@ -51,11 +52,13 @@ function(gmx_detect_avx_512_fma_units RESULT)
# Find flags required for AVX-512
gmx_find_simd_avx_512_flags(SIMD_AVX_512_C_SUPPORTED SIMD_AVX_512_CXX_SUPPORTED
SIMD_AVX_512_C_FLAGS SIMD_AVX_512_CXX_FLAGS)
# Find flag for GCC inline assembly
gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
if(${SIMD_AVX_512_CXX_SUPPORTED})
if(SIMD_AVX_512_CXX_SUPPORTED AND GMX_X86_GCC_INLINE_ASM)
# Compile the detection program
set(_compile_definitions "-I${PROJECT_SOURCE_DIR}/src -DGMX_IDENTIFY_AVX512_FMA_UNITS_STANDALONE ${SIMD_AVX_512_CXX_FLAGS} ${GMX_STDLIB_CXX_FLAGS}")
set(_compile_definitions "-I${PROJECT_SOURCE_DIR}/src -DGMX_IDENTIFY_AVX512_FMA_UNITS_STANDALONE -DSIMD_AVX_512_CXX_SUPPORTED=1 -DGMX_X86_GCC_INLINE_ASM=1 ${SIMD_AVX_512_CXX_FLAGS} ${GMX_STDLIB_CXX_FLAGS}")
try_compile(AVX_512_FMA_UNIT_DETECTION_COMPILED
"${PROJECT_BINARY_DIR}"
"${PROJECT_SOURCE_DIR}/src/gromacs/hardware/identifyavx512fmaunits.cpp"
......@@ -67,6 +70,8 @@ function(gmx_detect_avx_512_fma_units RESULT)
message(STATUS "Could not identify number of AVX-512 units - detection program did not compile")
endif()
set(RUN_AVX_512_FMA_UNIT_DETECTION_COMPILATION_QUIETLY TRUE CACHE INTERNAL "Keep quiet on any future compilation attempts")
else()
message(STATUS "Could not identify number of AVX-512 units - detection program missing compilation prerequisites")
endif()
if(AVX_512_FMA_UNIT_DETECTION_COMPILED)
......
......@@ -88,9 +88,9 @@ function(gmx_suggest_simd _suggested_simd)
endif()
set(OUTPUT_SIMD "AVX2_256")
else()
if (NOT SUGGEST_SIMD_QUIETLY)
message(WARNING "Could not run code to detect number of AVX-512 FMA units - assuming 2.")
endif()
if (NOT SUGGEST_SIMD_QUIETLY)
message(STATUS "Could not run code to detect number of AVX-512 FMA units - assuming 2.")
endif()
set(OUTPUT_SIMD "AVX_512")
endif()
elseif(CPU_DETECTION_FEATURES MATCHES " avx2 ")
......
......@@ -191,7 +191,7 @@ set(GMX_VERSION_PATCH 0)
# candidates, where it signifies the most recent such release from
# this branch; it will be empty before the first such release, as well
# as after the final release is out.
set(GMX_VERSION_SUFFIX "-beta2")
set(GMX_VERSION_SUFFIX "-beta3")
# Conventionally with libtool, any ABI change must change the major
# version number, the minor version number should change if it's just
......@@ -226,7 +226,7 @@ endif()
set(REGRESSIONTEST_VERSION "${GMX_VERSION_STRING}")
set(REGRESSIONTEST_BRANCH "refs/heads/release-2018")
set(REGRESSIONTEST_MD5SUM "ebfdb7f7b0c70a03038655ee12b18300" CACHE INTERNAL "MD5 sum of the regressiontests tarball")
set(REGRESSIONTEST_MD5SUM "c43d6db286ae52696ac595c43b081c23" CACHE INTERNAL "MD5 sum of the regressiontests tarball")
math(EXPR GMX_VERSION_NUMERIC
"${GMX_VERSION_MAJOR}*10000 + ${GMX_VERSION_PATCH}")
......
......@@ -374,7 +374,26 @@ Unfortunately reality is not that simple. Some algorithms like lattice
summation need quartets of elements, so even when the SIMD width is >4 we
need width-4 SIMD if it is supported. The availability of SIMD4 is indicated
by \ref GMX_SIMD4_HAVE_FLOAT and \ref GMX_SIMD4_HAVE_DOUBLE. For now we only
support a small subset of SIMD operations for SIMD4.
support a small subset of SIMD operations for SIMD4. Because SIMD4 doesn't
scale with increasingly large SIMD width it should be avoided for all new
code and SIMD4N should be used instead.
SIMD4N implementation
---------------------
Some code, like lattice summation, has inner loops which are smaller
than the full SIMD width. In GROMACS algorithms 3 and 4 iterations are common
because of PME order and three dimensions. This makes 4 an important special
case. Vectorizing such loops efficiently requires to collapse the two
most inner loops and using e.g. one 8-wide SIMD vector for 2 outer
and 4 inner iterations or one 16-wide SIMD vector for 4 outer and 4 inner
iterations. For this SIMD4N functions are
provided. The availability of these function is indicated by
\ref GMX_SIMD_HAVE_4NSIMD_UTIL_FLOAT and
\ref GMX_SIMD_HAVE_4NSIMD_UTIL_DOUBLE.
These functions return the type alias Simd4NFloat / Simd4NDouble which is
either the normal SIMD type or the SIMD4 type and thus only supports
the operations the SIMD4 type supports.
Predefined SIMD preprocessor macros
===================================
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANADOCK" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-ANADOCK" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-anadock \- Cluster structures from Autodock runs
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANAEIG" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-ANAEIG" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-anaeig \- Analyze eigenvectors/normal modes
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANALYZE" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-ANALYZE" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-analyze \- Analyze data sets
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ANGLE" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-ANGLE" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-angle \- Calculate distributions and correlations for angles and dihedrals
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-AWH" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-AWH" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-awh \- Extract data from an accelerated weight histogram (AWH) run
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-BAR" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-BAR" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-bar \- Calculate free energy difference estimates through Bennett's acceptance ratio
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-BUNDLE" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-BUNDLE" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-bundle \- Analyze bundles of axes, e.g., helices
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CHECK" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-CHECK" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-check \- Check and compare files
.
......@@ -70,8 +70,11 @@ virtual sites. With these flags, \fBgmx check\fP provides a quick check for such
.sp
The program can compare two run input (\&.tpr)
files
when both \fB\-s1\fP and \fB\-s2\fP are supplied.
Similarly a pair of trajectory files can be compared (using the \fB\-f2\fP
when both \fB\-s1\fP and \fB\-s2\fP are supplied. When comparing
run input files this way, the default relative tolerance is reduced
to 0.000001 and the absolute tolerance set to zero to find any differences
not due to minor compiler optimization differences, although you can
of course still set any other tolerances through the options.Similarly a pair of trajectory files can be compared (using the \fB\-f2\fP
option), or a pair of energy files (using the \fB\-e2\fP option).
.sp
For free energy simulations the A and B state topology from one
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CHI" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-CHI" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-chi \- Calculate everything you want to know about chi and other dihedrals
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CLUSTER" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-CLUSTER" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-cluster \- Cluster structures
.
......@@ -152,7 +152,7 @@ Options to specify input files:
.B \fB\-f\fP [<.xtc/.trr/…>] (traj.xtc) (Optional)
Trajectory: xtc trr cpt gro g96 pdb tng
.TP
.B \fB\-s\fP [<.tpr/.gro/…>] (topol.tpr) (Optional)
.B \fB\-s\fP [<.tpr/.gro/…>] (topol.tpr)
Structure+mass(db): tpr gro g96 pdb brk ent
.TP
.B \fB\-n\fP [<.ndx>] (index.ndx) (Optional)
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CLUSTSIZE" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-CLUSTSIZE" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-clustsize \- Calculate size distributions of atomic clusters
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CONFRMS" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-CONFRMS" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-confrms \- Fit two structures and calculates the RMSD
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CONVERT-TPR" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-CONVERT-TPR" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-convert-tpr \- Make a modifed run-input file
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-COVAR" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-COVAR" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-covar \- Calculate and diagonalize the covariance matrix
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-CURRENT" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-CURRENT" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-current \- Calculate dielectric constants and current autocorrelation function
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DENSITY" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-DENSITY" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-density \- Calculate the density of the system
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DENSMAP" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-DENSMAP" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-densmap \- Calculate 2D planar or axial-radial density maps
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DENSORDER" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-DENSORDER" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-densorder \- Calculate surface fluctuations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DIELECTRIC" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-DIELECTRIC" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-dielectric \- Calculate frequency dependent dielectric constants
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-DIPOLES" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-DIPOLES" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-dipoles \- Compute the total dipole plus fluctuations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DISRE" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-DISRE" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-disre \- Analyze distance restraints
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DISTANCE" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-DISTANCE" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-distance \- Calculate distances between pairs of positions
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DO_DSSP" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-DO_DSSP" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-do_dssp \- Assign secondary structure and calculate solvent accessible surface area
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-DOS" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-DOS" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-dos \- Analyze density of states and properties based on that
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DUMP" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-DUMP" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-dump \- Make binary files human readable
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DYECOUPL" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-DYECOUPL" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-dyecoupl \- Extract dye dynamics from trajectories
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-DYNDOM" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-DYNDOM" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-dyndom \- Interpolate and extrapolate structure rotations
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-EDITCONF" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-EDITCONF" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-editconf \- Convert and manipulates structure files
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-ENECONV" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-ENECONV" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-eneconv \- Convert energy files
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ENEMAT" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-ENEMAT" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-enemat \- Extract an energy matrix from an energy file
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-ENERGY" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-ENERGY" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-energy \- Writes energies to xvg files and display averages
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-FILTER" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-FILTER" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-filter \- Frequency filter trajectories, useful for making smooth movies
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-FREEVOLUME" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-FREEVOLUME" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-freevolume \- Calculate free volume
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-GANGLE" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-GANGLE" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-gangle \- Calculate angles
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-GENCONF" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-GENCONF" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-genconf \- Multiply a conformation in 'random' orientations
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-GENION" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-GENION" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-genion \- Generate monoatomic ions on energetically favorable positions
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-GENRESTR" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-GENRESTR" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-genrestr \- Generate position restraints or distance restraints for index groups
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-GROMPP" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-GROMPP" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-grompp \- Make a run input file
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-GYRATE" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-GYRATE" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-gyrate \- Calculate the radius of gyration
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-H2ORDER" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-H2ORDER" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-h2order \- Compute the orientation of water molecules
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-HBOND" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-HBOND" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-hbond \- Compute and analyze hydrogen bonds
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-HELIX" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-HELIX" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-helix \- Calculate basic properties of alpha helices
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-HELIXORIENT" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-HELIXORIENT" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-helixorient \- Calculate local pitch/bending/rotation/orientation inside helices
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-HELP" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-HELP" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-help \- Print help information
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-HYDORDER" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-HYDORDER" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-hydorder \- Compute tetrahedrality parameters around a given atom
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-INSERT-MOLECULES" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-INSERT-MOLECULES" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-insert-molecules \- Insert molecules into existing vacancies
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-LIE" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-LIE" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-lie \- Estimate free energy from linear combinations
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-MAKE_EDI" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-MAKE_EDI" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-make_edi \- Generate input files for essential dynamics sampling
.
......
.\" Man page generated from reStructuredText.
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.TH "GMX-MAKE_NDX" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-MAKE_NDX" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-make_ndx \- Make index files
.
......
.\" Man page generated from reStructuredText.
.
.TH "GMX-MDMAT" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-MDMAT" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-mdmat \- Calculate residue contact maps
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.TH "GMX-MDRUN" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-MDRUN" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-mdrun \- Perform a simulation, do a normal mode analysis or an energy minimization
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.TH "GMX-MINDIST" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-MINDIST" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-mindist \- Calculate the minimum distance between two groups
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.TH "GMX-MK_ANGNDX" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-MK_ANGNDX" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-mk_angndx \- Generate index files for 'gmx angle'
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.TH "GMX-MORPH" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-MORPH" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-morph \- Interpolate linearly between conformations
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.TH "GMX-MSD" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-MSD" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-msd \- Calculates mean square displacements
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.TH "GMX-NMEIG" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-NMEIG" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-nmeig \- Diagonalize the Hessian for normal mode analysis
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.TH "GMX-NMENS" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-NMENS" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-nmens \- Generate an ensemble of structures from the normal modes
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.TH "GMX-NMR" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-NMR" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-nmr \- Analyze nuclear magnetic resonance properties from an energy file
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.TH "GMX-NMTRAJ" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-NMTRAJ" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-nmtraj \- Generate a virtual oscillating trajectory from an eigenvector
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.TH "GMX-ORDER" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-ORDER" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-order \- Compute the order parameter per atom for carbon tails
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.TH "GMX-PAIRDIST" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-PAIRDIST" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-pairdist \- Calculate pairwise distances between groups of positions
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.TH "GMX-PDB2GMX" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-PDB2GMX" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-pdb2gmx \- Convert coordinate files to topology and FF-compliant coordinate files
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.TH "GMX-PME_ERROR" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-PME_ERROR" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-pme_error \- Estimate the error of using PME with a given input file
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.TH "GMX-POLYSTAT" "1" "Dec 11, 2017" "2018-beta2" "GROMACS"
.TH "GMX-POLYSTAT" "1" "Dec 19, 2017" "2018-beta3" "GROMACS"
.SH NAME
gmx-polystat \- Calculate static properties of polymers
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