Commit 6618c59f authored by Nicholas Breen's avatar Nicholas Breen

* man/demux.1, man/xplor2gmx.1: Restore.

* man/mdrun_mpi.{openmpi,mpich}.1: Resynchronize with master mdrun.1.
* control: Replace Conflicts: with Breaks: where appropriate.
* rules: Finally finish bashing CMake into shape.
parent 38640662
......@@ -3,15 +3,17 @@ gromacs (4.5.2-1) unstable; urgency=low
* Major new upstream release.
* All patches incorporated upstream and removed, except the Debian-
specific bug reporting portion of 11_readme.dpatch.
* man/{demux.1, xplor2gmx.1, gromacs.7}: incorporated upstream.
* man/gromacs.7: incorporated upstream, removed from Debian patch.
* man/luck.1: Rename to g_luck.1 and edit to reflect new name.
* man/mdrun_mpi.*.1: Resynchronize with upstream mdrun.1.
* watch: Update to recognize -betaX tarballs and ignore -GPU builds.
* rules: Convert from autotools to new CMake build system.
* control:
- Add Build-Depends on libxml2-dev.
- Update Standards-Version to 3.9.1.
- Replace Conflicts: with Breaks:.
-- Nicholas Breen <nbreen@ofb.net> Sat, 30 Oct 2010 15:16:42 -0700
-- Nicholas Breen <nbreen@ofb.net> Wed, 03 Nov 2010 17:39:52 -0700
gromacs (4.0.7-3) unstable; urgency=low
......
......@@ -15,7 +15,7 @@ Architecture: any
Section: science
Depends: gromacs-data (= ${source:Version}), ${shlibs:Depends}, ${misc:Depends}
Recommends: cpp
Conflicts: radiance (<= 3R8+20070924.dfsg-1)
Breaks: radiance (<= 3R8+20070924.dfsg-1)
Description: Molecular dynamics simulator, with building and analysis tools
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate
the Newtonian equations of motion for systems with hundreds to millions of
......@@ -36,7 +36,8 @@ Architecture: all
Section: science
Recommends: gromacs
Suggests: tcsh | c-shell
Conflicts: gromacs-doc, gromacs (<< 3.3.3-1)
Conflicts: gromacs-doc
Breaks: gromacs (<< 3.3.3-1)
Replaces: gromacs-doc
Description: GROMACS molecular dynamics sim, data and documentation
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate
......
......@@ -79,6 +79,8 @@ gromacs: binary-without-manpage usr/bin/g_helix
gromacs: binary-without-manpage usr/bin/g_helix_d
gromacs: binary-without-manpage usr/bin/g_helixorient
gromacs: binary-without-manpage usr/bin/g_helixorient_d
gromacs: binary-without-manpage usr/bin/g_kinetics
gromacs: binary-without-manpage usr/bin/g_kinetics_d
gromacs: binary-without-manpage usr/bin/g_lie
gromacs: binary-without-manpage usr/bin/g_lie_d
gromacs: binary-without-manpage usr/bin/g_luck
......
.TH "demux" "1" "13 Oct 2008" "GROMACS suite, Version 4.0"
.SH NAME
demux \- Convert XPLOR distance restraints to Gromacs format
.SH SYNOPSIS
\f3demux\fP
.B "md0.log "
.B "extra "
.SH DESCRIPTION
If you would like to make your trajectories continuous again you can use
.B demux
to read your md0.log file (you can
concatenate several if necessary) and produce a few output files. One of these
is a .xvg file (\fIreplica_ndx.xvg\fR) that can be passed to
.BR trjcat(1)
along with the
original trajectory files, in order to produce continuous trajectories. The
other file (\fIreplica_temp.xvg\fR) contains the temperatures for each replica,
starting at the original temperature. So if your replica of interest starts at,
say, 300 K, you can follow its trajectory through temperature space. It would
be interesting to add some functionality to make histograms of temperature
distributions for each replica, which according to most authors, should be
flat. The demuxed trajectories can be used with
.BR g_kinetics(1)
to obtain protein folding kinetics from REMD trajectories.
.SH OPTIONS
.B md0.log
Log file of the trajectory run you wish to make continuous. Multiple files can
be appended together.
.B extra
Number of times each entry in the log file will be copied. (Integer)
.SH LIMITATIONS
If your exchange was every N ps and you saved every M ps you can make for
the missing frames by setting \fBextra\fR to (N/M - 1). If N/M is not integer,
you're out of luck and you will not be able to demux your trajectories at all.
.SH SEE ALSO
.BR gromacs (7),
.BR trjcat (1),
.BR g_kinetics (1),
.I <http://wiki.gromacs.org/index.php/REMD>
This diff is collapsed.
This diff is collapsed.
.TH "xplor2gmx" "1" "13 Oct 2008" "GROMACS suite, Version 4.0"
.SH NAME
xplor2gmx \- Convert XPLOR distance restraints to Gromacs format
.SH SYNOPSIS
\f3xplor2gmx\fP
.BI "(residue offset)" ""
.BI " input.pdb " ""
.SH DESCRIPTION
.B xplor2gmx
reads an XPLOR input file with distance restraint data
as sometimes is found in the pdb database (http://www.pdb.org).
From this input file dihedral restrints should be removed, such that
only distance restraints are left. The script can handle ambiguous restraints.
It converts the distance restraints to GROMACS format.
A restraints file (.dat) should be provided on STDIN, and a suitable
output file (.itp) is sent to STDOUT.
.SH EXAMPLES
xplor2gmx.pl 33 conf.pdb < restraints.dat > disre.itp
.SH OPTIONS
.B xplor2gmx
requires two command line options: first, the residue offset (integer);
second, the .pdb filename. The pdb file must have correct atom numbers.
.SH SEE ALSO
.BR gromacs (7)
......@@ -47,7 +47,6 @@ OPENMPI_CONFIG_PARAMS = \
-DGMX_MPI=ON \
-DGMX_THREADS=OFF \
-DGMX_DEFAULT_SUFFIX=FALSE
-DGMX_LIBS_SUFFIX=_mpi_openmpi \
-DGMX_FORTRAN=OFF \
-DGMX_X11=OFF \
-DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib/openmpi/lib $(LDFLAGS)"
......@@ -67,15 +66,17 @@ endif
configure: patch-stamp configure-stamp
configure-stamp: patch-stamp
dh_testdir
(mkdir -p build/basic; cd build/basic; cmake $(COMMON_CONFIG_PARAMS))
(mkdir -p build/basic-dp; cd build/basic-dp; cmake $(COMMON_CONFIG_PARAMS) -DGMX_DOUBLE=ON)
(mkdir -p build/basic; cd build/basic; cmake $(COMMON_CONFIG_PARAMS) -DGMX_MPI=OFF)
(mkdir -p build/basic-dp; cd build/basic-dp; cmake $(COMMON_CONFIG_PARAMS) -DGMX_MPI=OFF -DGMX_DOUBLE=ON)
(mkdir -p build/mpich; cd build/mpich; CC=/usr/bin/mpicc.mpich2 cmake \
$(COMMON_CONFIG_PARAMS) $(MPICH_CONFIG_PARAMS) -DGMX_BINARY_SUFFIX="_mpi.mpich" -DGMX_LIBS_SUFFIX="_mpi.mpich")
(mkdir -p build/mpich-dp; cd build/mpich-dp; CC=/usr/bin/mpicc.mpich2 cmake \
$(COMMON_CONFIG_PARAMS) $(MPICH_CONFIG_PARAMS) -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.mpich" -DGMX_LIBS_SUFFIX="_mpi_d.mpich")
ifneq (,$(findstring $(DEB_HOST_ARCH),$(OPENMPI_ARCH)))
(mkdir -p build/openmpi; cd build/openmpi; CC=/usr/bin/mpicc.openmpi cmake $(COMMON_CONFIG_PARAMS) $(OPENMPI_CONFIG_PARAMS))
(mkdir -p build/openmpi-dp; cd build/openmpi-dp; CC=/usr/bin/mpicc.openmpi cmake $(COMMON_CONFIG_PARAMS) $(OPENMPI_CONFIG_PARAMS))
(mkdir -p build/openmpi; cd build/openmpi; CC=/usr/bin/mpicc.openmpi cmake \
$(COMMON_CONFIG_PARAMS) $(OPENMPI_CONFIG_PARAMS) -DGMX_BINARY_SUFFIX="_mpi.openmpi" -DGMX_LIBS_SUFFIX="_mpi.openmpi")
(mkdir -p build/openmpi-dp; cd build/openmpi-dp; CC=/usr/bin/mpicc.openmpi cmake \
$(COMMON_CONFIG_PARAMS) $(OPENMPI_CONFIG_PARAMS) -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.openmpi" -DGMX_LIBS_SUFFIX="_mpi_d.openmpi")
endif
touch $@
......@@ -178,6 +179,8 @@ install-basic: build
# man pages for a pair of Perl scripts are installed *after* the _d duplication,
# as they have no double-precision variants.
dh_installman -pgromacs debian/man/demux.1 debian/man/xplor2gmx.1
# this program is currently broken - keep it from shipping until fixed
rm $(CURDIR)/debian/gromacs/usr/bin/g_pme_error $(CURDIR)/debian/gromacs/usr/bin/g_pme_error_d
# three lintian warnings are overridden:
# - package-name-doesnt-match-sonames: the libraries are private to
# GROMACS, and it's unlikely that any new package will start using
......
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