Commit b4377eeb authored by Nicholas Breen's avatar Nicholas Breen

Merge experimental branch back into unstable

parent 03719416
gromacs (4.6.6-1) unstable; urgency=medium
* New upstream release. Final release of the 4.6 series.
* debian/copyright: Updated.
* patches/21_hurd.patch: Incorporated upstream, patch removed.
-- Nicholas Breen <nbreen@debian.org> Wed, 02 Jul 2014 18:11:14 -0700
gromacs (5.0-2) experimental; urgency=low
* Add 20_random123_platforms.patch to disable architecture check from
external Random123 code.
* Drop discussion of shared libraries from README.Debian for
gromacs-{mpich,openmpi}.
-- Nicholas Breen <nbreen@debian.org> Wed, 02 Jul 2014 20:13:01 -0700
gromacs (5.0-1) experimental; urgency=low
* New upstream release, experimental upload.
- g_sigeps / gmx sigeps command line handling no longer crashes on
invalid input (Closes: #715935).
* Rebase existing patches. Add new patches:
- 31_manpage_hyphenation.patch: Some parts of the man page generation
get the hyphen/dash separation right, some don't. A temporary fix
pending significant overhaul of the man page system.
<http://redmine.gromacs.org/issues/1437>
- 32_spelling.patch: Correction of minor spelling errors.
* man/g_{dos,kinetics,luck}.1: Incorporated upstream, removed.
* man/gmx.1: Rudimentary man page written and added.
* man/mdrun_mpi.*.1: Updated with text from upstream gmx-mpich.1.
* rules: Updates for MPI builds and assorted upstream changes.
* gromacs-data.lintian-overrides, source/lintian-overrides: Removed.
* Add Build-Depends on external libboost-dev.
* Switch away from hardening-wrapper in favor of dpkg-buildflags.
* Update copyright file.
-- Nicholas Breen <nbreen@debian.org> Wed, 02 Jul 2014 17:35:18 -0700
gromacs (4.6.5-2) unstable; urgency=medium
......
......@@ -3,7 +3,7 @@ Section: science
Priority: extra
Maintainer: Debichem Team <debichem-devel@lists.alioth.debian.org>
Uploaders: Nicholas Breen <nbreen@debian.org>
Build-Depends: debhelper (>= 7.0.0), libfftw3-dev, libmpich-dev (>= 3), libopenmpi-dev (>= 1.2.4-5) [alpha amd64 arm64 armel armhf hurd-i386 i386 ia64 kfreebsd-amd64 kfreebsd-i386 mips mips64 mips64el mipsel powerpc powerpcspe ppc64 ppc64el sparc sparc64], libx11-dev, zlib1g-dev, libgsl0-dev, libxml2-dev, libblas-dev, liblapack-dev, cmake, hardening-wrapper
Build-Depends: debhelper (>= 7.0.0), libfftw3-dev, libmpich-dev (>= 3.0.4-6), libopenmpi-dev (>= 1.2.4-5) [alpha amd64 arm64 armel armhf hurd-i386 i386 ia64 kfreebsd-amd64 kfreebsd-i386 mips mips64 mips64el mipsel powerpc powerpcspe ppc64 ppc64el sparc sparc64], libx11-dev, zlib1g-dev, libgsl0-dev, libxml2-dev, libblas-dev, liblapack-dev, libboost-dev, cmake
Standards-Version: 3.9.5
Homepage: http://www.gromacs.org/
Vcs-Browser: http://anonscm.debian.org/viewvc/debichem/
......@@ -24,13 +24,10 @@ Description: Molecular dynamics simulator, with building and analysis tools
extremely fast at calculating the nonbonded interactions (that usually
dominate simulations) many groups are also using it for research on non-
biological systems, e.g. polymers.
.
GROMACS offers entirely too many features for a brief description to do it
justice. A more complete listing is available at
<http://www.gromacs.org/content/view/12/176/>.
Package: gromacs-data
Architecture: all
Depends: ${misc:Depends}
Recommends: gromacs
Suggests: tcsh | c-shell
Conflicts: gromacs-doc
......
......@@ -27,7 +27,7 @@ of the License, or (at your option) any later version.
A detailed list of Gromacs contributors is available at
http://www.gromacs.org/About_Gromacs/People
=================================================
============================================
GROMACS is free software, distributed under the GNU Lesser General
Public License (LGPL) Version 2.1. See section 1 for details. GROMACS
......@@ -46,6 +46,12 @@ This file contains the licenses for the following bodies of code:
5. thread_mpi
6. Blas
7. Lapack
8. Subset of Boost C++ library
9. Google Test and Google Mock
10. Sun XDR implementation (External Data Representation)
11. Sun FDLIBM (Freely Distributable Maths Library)
12. Random123
13. md5
Our chosen method for packaging distributions (CPack) only permits a
package to have a single license file, so we are unfortunately forced
......@@ -55,6 +61,7 @@ about that.
============================================
1. GROMACS
==========
As our use of the LGPL conveys upon a licensee the option to
redistribute the library under the terms of the plain GPL, we must
......@@ -79,11 +86,8 @@ same licensing conditions as GROMACS proper.
2. Trajectory file reading using VMD plugins
============================================
Files: include/molfile_plugin.h
include/vmddlopen.h
include/vmdplugin.h
src/gmxlib/vmddlopen.c
src/gmxlib/vmdio.c
Files: src/external/vmd_molfile/
src/gromacs/fileio/vmdio.c
(C) Copyright 1995-2009 The Board of Trustees of the
University of Illinois
......@@ -123,7 +127,7 @@ OTHER DEALINGS WITH THE SOFTWARE.
3. Internal FFT (ffpack)
========================
Files: src/mdlib/fftpack.c
Files: src/external/fftpack/fftpack.c
Copyright (c) 2005-2011, NumPy Developers.
All rights reserved.
......@@ -162,6 +166,8 @@ Algorithmically based on Fortran-77 FFTPACK by Paul N. Swarztrauber (Version 4,
4. The memtestG80 library
=========================
Files: src/gromacs/gmxlib/gpu_utils/memtestG80_core.*
The memtestG80 library, written by Imran Haque, is Copyright 2009 Stanford University,
covered by the LGPL license. It may be used under the following terms:
......@@ -191,6 +197,8 @@ available at http://www.gnu.org/licenses/lgpl-3.0.txt or on this system at
5. thread_mpi
=============
Files: src/external/thread_mpi/
Copyright (c) 2009-2012, Sander Pronk & Erik Lindahl.
All rights reserved.
......@@ -270,3 +278,171 @@ in Gromacs (primarily full & sparse matrix diagonalization), so in most cases it
better idea to use the full reference implementation.
Erik Lindahl, 2008-10-07.
8. Subset of Boost C++ library
==============================
Files: src/external/boost/boost/*
Boost Software License - Version 1.0 - August 17th, 2003
Permission is hereby granted, free of charge, to any person or organization
obtaining a copy of the software and accompanying documentation covered by
this license (the "Software") to use, reproduce, display, distribute,
execute, and transmit the Software, and to prepare derivative works of the
Software, and to permit third-parties to whom the Software is furnished to
do so, all subject to the following:
The copyright notices in the Software and this entire statement, including
the above license grant, this restriction and the following disclaimer,
must be included in all copies of the Software, in whole or in part, and
all derivative works of the Software, unless such copies or derivative
works are solely in the form of machine-executable object code generated by
a source language processor.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE.
9. Google Test and Google Mock
===============================
Files: src/external/gmock-1.7.0/*
Copyright 2008, Google Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above
copyright notice, this list of conditions and the following disclaimer
in the documentation and/or other materials provided with the
distribution.
* Neither the name of Google Inc. nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
10. Sun Extensible Data Representation routines (XDR)
=====================================================
Files: src/gromacs/fileio/gmx_system_xdr.c
Sun RPC is a product of Sun Microsystems, Inc. and is provided for
unrestricted use provided that this legend is included on all tape
media and as a part of the software program in whole or part. Users
may copy or modify Sun RPC without charge, but are not authorized
to license or distribute it to anyone else except as part of a product or
program developed by the user.
SUN RPC IS PROVIDED AS IS WITH NO WARRANTIES OF ANY KIND INCLUDING THE
WARRANTIES OF DESIGN, MERCHANTIBILITY AND FITNESS FOR A PARTICULAR
PURPOSE, OR ARISING FROM A COURSE OF DEALING, USAGE OR TRADE PRACTICE.
Sun RPC is provided with no support and without any obligation on the
part of Sun Microsystems, Inc. to assist in its use, correction,
modification or enhancement.
SUN MICROSYSTEMS, INC. SHALL HAVE NO LIABILITY WITH RESPECT TO THE
INFRINGEMENT OF COPYRIGHTS, TRADE SECRETS OR ANY PATENTS BY SUN RPC
OR ANY PART THEREOF.
In no event will Sun Microsystems, Inc. be liable for any lost revenue
or profits or other special, indirect and consequential damages, even if
Sun has been advised of the possibility of such damages.
Sun Microsystems, Inc.
2550 Garcia Avenue
Mountain View, California 94043
11. Sun FDLIBM (Freely Distributable Maths Library)
===================================================
Files: src/gromacs/math/utilities.c
Copyright (C) 1993 by Sun Microsystems, Inc. All rights reserved.
Developed at SunSoft, a Sun Microsystems, Inc. business.
Permission to use, copy, modify, and distribute this
software is freely granted, provided that this notice
is preserved.
12. Random123
============================================
Copyright 2010-2012, D. E. Shaw Research.
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are
met:
* Redistributions of source code must retain the above copyright
notice, this list of conditions, and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright
notice, this list of conditions, and the following disclaimer in the
documentation and/or other materials provided with the distribution.
* Neither the name of D. E. Shaw Research nor the names of its
contributors may be used to endorse or promote products derived from
this software without specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
13. md5
============================================
Copyright (C) 1999, 2002 Aladdin Enterprises. All rights reserved.
This software is provided 'as-is', without any express or implied
warranty. In no event will the authors be held liable for any damages
arising from the use of this software.
Permission is granted to anyone to use this software for any purpose,
including commercial applications, and to alter it and redistribute it
freely, subject to the following restrictions:
1. The origin of this software must not be misrepresented; you must not
claim that you wrote the original software. If you use this software
in a product, an acknowledgment in the product documentation would be
appreciated but is not required.
2. Altered source versions must be plainly marked as such, and must not be
misrepresented as being the original software.
3. This notice may not be removed or altered from any source distribution.
L. Peter Deutsch
ghost@aladdin.com
# demo scripts
# gromacs-data: script-not-executable
usr/bin
usr/share/man/man1
usr/share/gromacs/shell-specific
gromacs-mpich: package-name-doesnt-match-sonames
# Adaptive Resolution Molecular Dynamics Simulation
gromacs-mpich: spelling-error-in-binary usr/lib/libgmxpreprocess_mpi.mpich.so.8 AdResS Address
gromacs-mpich: spelling-error-in-binary usr/lib/libgmxpreprocess_mpi_d.mpich.so.8 AdResS Address
gromacs-mpich: spelling-error-in-binary usr/lib/libmd_mpi.mpich.so.8 AdResS Address
gromacs-mpich: spelling-error-in-binary usr/lib/libmd_mpi_d.mpich.so.8 AdResS Address
gromacs-mpich: spelling-error-in-binary usr/lib/libgmx_mpi.mpich.so.8 AdResS Address
gromacs-mpich: spelling-error-in-binary usr/lib/libgmx_mpi_d.mpich.so.8 AdResS Address
# too small to merit a -dev package of its own
gromacs-mpich: non-dev-pkg-with-shlib-symlink
gromacs-mpich: spelling-error-in-binary usr/bin/mdrun_mpi.mpich AdresS Address
gromacs-mpich: spelling-error-in-binary usr/bin/mdrun_mpi_d.mpich AdresS Address
# Seems to be a version-specific, platform-specific false positive; not in source
gromacs-mpich [amd64]: spelling-error-in-binary usr/bin/mdrun_mpi.mpich tEH the
gromacs-mpich [amd64]: spelling-error-in-binary usr/bin/mdrun_mpi_d.mpich tEH the
usr/bin
usr/share/man/man1
usr/share/lintian/overrides
usr/share/gromacs/shell-specific
gromacs-openmpi: package-name-doesnt-match-sonames
# Adaptive Resolution Molecular Dynamics Simulation
gromacs-openmpi: spelling-error-in-binary usr/lib/libgmxpreprocess_mpi.openmpi.so.8 AdResS Address
gromacs-openmpi: spelling-error-in-binary usr/lib/libgmxpreprocess_mpi_d.openmpi.so.8 AdResS Address
gromacs-openmpi: spelling-error-in-binary usr/lib/libmd_mpi.openmpi.so.8 AdResS Address
gromacs-openmpi: spelling-error-in-binary usr/lib/libmd_mpi_d.openmpi.so.8 AdResS Address
gromacs-openmpi: spelling-error-in-binary usr/lib/libgmx_mpi.openmpi.so.8 AdResS Address
gromacs-openmpi: spelling-error-in-binary usr/lib/libgmx_mpi_d.openmpi.so.8 AdResS Address
# too small to merit a -dev package of its own
non-dev-pkg-with-shlib-symlink
gromacs-openmpi: spelling-error-in-binary usr/bin/mdrun_mpi.openmpi AdresS Address
gromacs-openmpi: spelling-error-in-binary usr/bin/mdrun_mpi_d.openmpi AdresS Address
# Seems to be a version-specific, platform-specific false positive; not in source
gromacs-openmpi [amd64]: spelling-error-in-binary usr/bin/mdrun_mpi.openmpi tEH the
gromacs-openmpi [amd64]: spelling-error-in-binary usr/bin/mdrun_mpi_d.openmpi tEH the
......@@ -11,19 +11,5 @@ in parallel. In this case, the OpenMPI build will take priority as
the default version (the one that controls the mdrun_mpi alias) --
you may change this with update-alternatives(8).
One minor consequence of this design is that third-party applications
that link to the GROMACS MPI-enabled shared libraries will not work
without setting up compatibility symlinks, nor will such binaries
compiled on Debian systems work elsewhere. I am not currently aware
of any such applications, but in case you've got any, here's what you
need to know:
* /usr/lib/libgmx_mpi.so has been renamed to libgmx_mpi_#MPIABBR#.so
* /usr/lib/libmd_mpi.so has been renamed to libmd_mpi_#MPIABBR#.so
* The library SONAMEs have changed accordingly
* The same transformations have been applied to the static libraries
(.a extensions)
* The non-MPI libraries in the gromacs and gromacs-dev packages are
unaffected.
-- Nicholas Breen <nbreen@ofb.net>, Fri, 21 Oct 2005 11:27:27 -0400
-- Nicholas Breen <nbreen@debian.org>, Fri, 21 Oct 2005 11:27:27 -0400
revised Wed, 02 Jul 2014 20:11:25 -0700
This diff is collapsed.
# no need to split out the libraries into separate lib packages,
# since no other package uses them
# or to generate symbol files, since no other package uses them
gromacs: package-name-doesnt-match-sonames
gromacs: no-symbols-control-file
# Adaptive Resolution Molecular Dynamics Simulation
gromacs: spelling-error-in-binary usr/bin/grompp AdResS Address
gromacs: spelling-error-in-binary usr/bin/grompp_d AdResS Address
gromacs: spelling-error-in-binary usr/lib/libgmxpreprocess.so.8 AdResS Address
gromacs: spelling-error-in-binary usr/lib/libgmxpreprocess_d.so.8 AdResS Address
gromacs: spelling-error-in-binary usr/lib/libmd.so.8 AdResS Address
gromacs: spelling-error-in-binary usr/lib/libmd_d.so.8 AdResS Address
gromacs: spelling-error-in-binary usr/lib/libgmx.so.8 AdResS Address
gromacs: spelling-error-in-binary usr/lib/libgmx_d.so.8 AdResS Address
gromacs: spelling-error-in-binary usr/lib/*/libgromacs.so.0.0.0 AdResS Address
gromacs: spelling-error-in-binary usr/lib/*/libgromacs_d.so.0.0.0 AdResS Address
# Seems to be a version-specific, platform-specific false positive; not in source
gromacs [amd64]: spelling-error-in-binary usr/lib/x86_64-linux-gnu/libgromacs.so.0.0.0 tEH the
gromacs [amd64]: spelling-error-in-binary usr/lib/x86_64-linux-gnu/libgromacs_d.so.0.0.0 tEH the
.TH g_dos 1 "Wed 21 Sep 2011" "" "GROMACS suite, VERSION 4.5.5"
.SH NAME
g_dos \- compute density of states from a simulation trajectory
.B VERSION 4.5.5
.SH SYNOPSIS
\f3g_dos\fP
.BI "\-f" " traj.trr "
.BI "\-s" " topol.tpr "
.BI "\-n" " index.ndx "
.BI "\-vacf" " vacf.xvg "
.BI "\-mvacf" " mvacf.xvg "
.BI "\-dos" " dos.xvg "
.BI "\-g" " dos.log "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-[no]v" ""
.BI "\-[no]recip" ""
.BI "\-[no]abs" ""
.BI "\-[no]normdos" ""
.BI "\-T" " real "
.BI "\-acflen" " int "
.BI "\-[no]normalize" ""
.BI "\-P" " enum "
.BI "\-fitfn" " enum "
.BI "\-ncskip" " int "
.BI "\-beginfit" " real "
.BI "\-endfit" " real "
.SH DESCRIPTION
\&\fB g_dos\fR computes the Density of States from a simulation.
\&In order for this to be meaningful the velocities must be saved
\&in the trajectory with sufficiently high frequency such as to cover
\&all vibrations. For flexible systems that would be around a few fs
\&between saving. Properties based on the DoS are printed on the
\&standard output.
.SH FILES
.BI "\-f" " traj.trr"
.B Input
Full precision trajectory: trr trj cpt
.BI "\-s" " topol.tpr"
.B Input
Run input file: tpr tpb tpa
.BI "\-n" " index.ndx"
.B Input, Opt.
Index file
.BI "\-vacf" " vacf.xvg"
.B Output
xvgr/xmgr file
.BI "\-mvacf" " mvacf.xvg"
.B Output
xvgr/xmgr file
.BI "\-dos" " dos.xvg"
.B Output
xvgr/xmgr file
.BI "\-g" " dos.log"
.B Output
Log file
.SH OTHER OPTIONS
.BI "\-[no]h" "no "
Print help info and quit
.BI "\-[no]version" "no "
Print version info and quit
.BI "\-nice" " int" " 19"
Set the nicelevel
.BI "\-b" " time" " 0 "
First frame (ps) to read from trajectory
.BI "\-e" " time" " 0 "
Last frame (ps) to read from trajectory
.BI "\-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
.BI "\-[no]w" "no "
View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files
.BI "\-xvg" " enum" " xmgrace"
xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR
.BI "\-[no]v" "yes "
Be loud and noisy.
.BI "\-[no]recip" "no "
Use cm\-1 on X\-axis instead of 1/ps for DoS plots.
.BI "\-[no]abs" "no "
Use the absolute value of the Fourier transform of the VACF as the Density of States. Default is to use the real component only
.BI "\-[no]normdos" "no "
Normalize the DoS such that it adds up to 3N. This is a hack that should not be necessary.
.BI "\-T" " real" " 298.15"
Temperature in the simulation
.BI "\-acflen" " int" " \-1"
Length of the ACF, default is half the number of frames
.BI "\-[no]normalize" "yes "
Normalize ACF
.BI "\-P" " enum" " 0"
Order of Legendre polynomial for ACF (0 indicates none): \fB 0\fR, \fB 1\fR, \fB 2\fR or \fB 3\fR
.BI "\-fitfn" " enum" " none"
Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR, \fB exp9\fR or \fB erffit\fR
.BI "\-ncskip" " int" " 0"
Skip N points in the output file of correlation functions
.BI "\-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
.BI "\-endfit" " real" " \-1 "
Time where to end the exponential fit of the correlation function, \-1 is until the end
.SH KNOWN PROBLEMS
\- This program needs a lot of memory: total usage equals the number of atoms times 3 times number of frames times 4 (or 8 when run in double precision).
.SH SEE ALSO
.BR gromacs(7)
More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
.TH "G_KINETICS" "1" "20 Aug 2008" "GROMACS suite, Version 3.3"
.SH NAME
g_kinetics \- estimate rate constants
.SH SYNOPSIS
.B g_kinetics
.BI "\-f" " temp.xvg "
.BI "\-d" " data.xvg "
.BI "\-o" " ft_all.xvg "
.BI "\-g" " remd.log "
.BI "\-m" " melt.xvg "
.I [other options...]
.SH DESCRIPTION
.B g_kinetics
reads two xvg files, each one containing data for N replicas.
The first file contains the temperature of each replica at each timestep
and the second contains real values that can be interpreted as
an indicator for folding. If the value in the file is larger than
the cutoff it is taken to be unfolded and the other way around.[PAR]
From these data an estimate of the forward and backward rate constants
for folding is made at a reference temperature. In addition,
a theoretical melting curve and free energy as a function of temperature
are printed in an xvg file.
The user can give a max value to be regarded as intermediate
(\fI\-ucut\fP), which, when given will trigger the use of an intermediate state
in the algorithm to be defined as those structures that have
cutoff < DATA < ucut. Structures with DATA values larger than ucut will
not be regarded as potential folders. In this case 8 parameters are optimized.
The average fraction folded is printed in an xvg file together with the fit to it.
If an intermediate is used a further file will show the build of the intermediate and the fit to that process.
The program can also be used with continuous variables (by setting
\fI\-nodiscrete\fP). In this case kinetics of other processes can be
studied. This is very much a work in progress and hence the manual
(this information) is lagging behind somewhat.
.SH FILES
.nf
Option Filename Type Description
------------------------------------------------------------
\-f temp.xvg Input xvgr/xmgr file
\-d data.xvg Input xvgr/xmgr file
\-d2 data2.xvg Input, Opt. xvgr/xmgr file
\-o ft_all.xvg Output xvgr/xmgr file
\-o2 it_all.xvg Output, Opt. xvgr/xmgr file
\-o3 ft_repl.xvg Output, Opt. xvgr/xmgr file
\-ee err_est.xvg Output, Opt. xvgr/xmgr file
\-g remd.log Output Log file
\-m melt.xvg Output xvgr/xmgr file
.fi
.SH OPTIONS
.nf
Option Type Value Description
------------------------------------------------------
\-[no]h bool no Print help info and quit
\-[no]X bool no Use dialog box GUI to edit command line options
\-nice int 19 Set the nicelevel
\-tu enum ps Time unit: ps, fs, ns, us, ms or s
\-[no]w bool no View output xvg, xpm, eps and pdb files
\-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
\-[no]time bool yes Expect a time in the input
\-b real 0 First time to read from set
\-e real 0 Last time to read from set
\-bfit real \-1 Time to start the fit from
\-efit real \-1 Time to end the fit
\-T real 298.15 Reference temperature for computing rate constants
\-n int 1 Read data for # replicas. Only necessary when
files are written in xmgrace format using @type
and & as delimiters.
\-cut real 0.2 Cut-off (max) value for regarding a structure as
folded
\-ucut real 0 Cut-off (max) value for regarding a structure as
intermediate (if not folded)
\-euf real 10 Initial guess for energy of activation for
folding (kJ/mole)
\-efu real 30 Initial guess for energy of activation for
unfolding (kJ/mole)
\-ei real 10 Initial guess for energy of activation for
intermediates (kJ/mole)
\-maxiter int 100 Max number of iterations
\-[no]back bool yes Take the back reaction into account
\-tol real 0.001 Absolute tolerance for convergence of the Nelder
and Mead simplex algorithm
\-skip int 0 Skip points in the output xvg file
\-[no]split bool yes Estimate error by splitting the number of
replicas in two and refitting
\-[no]sum bool yes Average folding before computing chi^2
\-[no]discrete bool yes Use a discrete folding criterium (F <-> U) or a
continuous one
\-mult int 1 Factor to multiply the data with before
discretization
.fi
.SH SEE ALSO
.BR gromacs (7)
.PP
More information about the \fBGROMACS\fR suite is available in
\fI/usr/share/doc/gromacs\fR or at \fI\%http://www.gromacs.org/\fR.
.PP
Implementation details have been published in Phys. Rev. Lett. 96, 238102 (2006),
<\fI\%http://dx.doi.org/10.1103/PhysRevLett.96.238102\fR>.
.\" Hey, EMACS: -*- nroff -*-
.\" First parameter, NAME, should be all caps
.\" Second parameter, SECTION, should be 1-8, maybe w/ subsection
.\" other parameters are allowed: see man(7), man(1)
.TH "G_LUCK" "1" "2 Oct 2010" "GROMACS suite, Version 4.5"
.\" Please adjust this date whenever revising the manpage.
.\"
.\" Some roff macros, for reference:
.\" .nh disable hyphenation
.\" .hy enable hyphenation
.\" .ad l left justify
.\" .ad b justify to both left and right margins
.\" .nf disable filling
.\" .fi enable filling
.\" .br insert line break
.\" .sp <n> insert n+1 empty lines
.\" for manpage-specific macros, see man(7)
.SH NAME
g_luck \- GROMACS installation test program
.SH SYNOPSIS
.B g_luck
.SH DESCRIPTION
.B g_luck
writes a randomly selected quote to \fIstdout\fP. Normally this
serves to test a freshly-compiled GROMACS installation; it also helps to
maintain that air of cultural sophistication and wide-ranging appeal that
characterizes any molecular dynamics package worth its force fields.
.SH OPTIONS
.B g_luck
takes no options\. It may vary its output depending on whether
the user is cool or not.
.SH SEE ALSO
.BR fortune (1),
.BR gromacs (7)
.SH AUTHOR
Sadly, the current GROMACS distribution lacks official documentation
for this command.
This manual page was written by Nicholas Breen <\&nbreen@ofb\.net\&>,
for the Debian GNU/Linux system (but may be used by others)\.
.TH GMX 1 "2014-07-02" "GROMACS 5.0"
.SH NAME
gmx \- master command for GROMACS suite
.SH SYNOPSIS
\fBgmx\fP \fI [ options ]\fP command \fI[ command options ... ]\fP
.SH DESCRIPTION
.B gmx
is the unified interface for nearly all GROMACS operations. For a list of
all available commands, run
.B gmx help command
, and for detailed help on a specific command, e.g. rms, run
.B gmx help rms
or read the (equivalent) man page for
.BR gmx-rms(1).
.PP
.SH SELECTION SYNTAX AND USAGE
Selections are used to select atoms/molecules/residues for analysis. In
contrast to traditional index files, selections can be dynamic, i.e., select
different atoms for different trajectory frames.
.PP
Each analysis tool requires a different number of selections and the
selections are interpreted differently. The general idea is still the same:
each selection evaluates to a set of positions, where a position can be an
atom position or center-of-mass or center-of-geometry of a set of atoms. The
tool then uses these positions for its analysis to allow very flexible
processing. Some analysis tools may have limitations on the types of
selections allowed.
.PP
To get started with selections, run, e.g., \fBgmx select\fP without specifying
selections on the command-line and use the interactive prompt to try out
different selections. This tool provides output options that allow one to see
what is actually selected by the given selections, and the interactive prompt
reports syntax errors immediately, allowing one to try again. The subtopics
listed below give more details on different aspects of selections.
.PP
Available subtopics:
.PD 0
.TP
\fIarithmetic\fP Arithmetic expressions in selections
.TP
\fIcmdline\fP Specifying selections from command line
.TP
\fIevaluation\fP Selection evaluation and optimization
.TP
\fIexamples\fP Selection examples
.TP
\fIkeywords\fP Selection keywords
.TP
\fIlimitations\fP Selection limitations
.TP
\fIpositions\fP Specifying positions in selections
.TP
\fIsyntax\fP Selection syntax
.PD
.PP
View these selections with \fBgmx help selection SUBTOPIC\fB.
.PP
.SH GLOBAL OPTIONS
For command specific options, see \fBgmx help COMMAND\fP.
.TP
.B \-h
Print help and quit.
.TP
.B \-quiet
Do not print common startup info or quotes.
.TP