Commit 38640662 authored by Nicholas Breen's avatar Nicholas Breen

Fix g_luck.1 typo, remove man/demux.1 & man/xplor2gmx/1 incorporated upstream

parent afcbaf43
......@@ -3,8 +3,9 @@ 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/gromacs.7: incorporated upstream.
* watch: update to recognize -betaX tarballs and ignore -GPU builds.
* man/{demux.1, xplor2gmx.1, gromacs.7}: incorporated upstream.
* man/luck.1: Rename to g_luck.1 and edit to reflect new name.
* 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.
......
.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>
.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)
......@@ -40,12 +40,13 @@ endif
MPICH_CONFIG_PARAMS = \
-DGMX_MPI=ON \
-DGMX_THREADS=OFF \
-DGMX_LIBS_SUFFIX=_mpi_mpich \
-DGMX_X11=OFF
-DGMX_X11=OFF \
-DGMX_DEFAULT_SUFFIX=FALSE
OPENMPI_CONFIG_PARAMS = \
-DGMX_MPI=ON \
-DGMX_THREADS=OFF \
-DGMX_DEFAULT_SUFFIX=FALSE
-DGMX_LIBS_SUFFIX=_mpi_openmpi \
-DGMX_FORTRAN=OFF \
-DGMX_X11=OFF \
......@@ -68,8 +69,10 @@ 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/mpich; cd build/mpich; CC=/usr/bin/mpicc.mpich2 cmake $(COMMON_CONFIG_PARAMS) $(MPICH_CONFIG_PARAMS))
(mkdir -p build/mpich-dp; cd build/mpich-dp; CC=/usr/bin/mpicc.mpich2 cmake $(COMMON_CONFIG_PARAMS) -DGMX_DOUBLE=ON $(MPICH_CONFIG_PARAMS))
(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))
......@@ -168,7 +171,7 @@ install-basic: build
$(MAKE) -C build/basic install DESTDIR=$(CURDIR)/debian/gromacs
$(MAKE) -C build/basic-dp install DESTDIR=$(CURDIR)/debian/gromacs
rm -f $(CURDIR)/debian/gromacs/usr/share/man/man1/*_d.1
dh_installman -pgromacs debian/man/luck.1
dh_installman -pgromacs debian/man/g_luck.1 debian/man/g_kinetics.1
for manpage in $(CURDIR)/debian/gromacs/usr/share/man/man1/*.1; do \
dh_link -pgromacs usr/share/man/man1/`basename $${manpage}` usr/share/man/man1/`basename $${manpage} .1`_d.1 ; \
done
......
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