Commit 7bb80ca9 authored by Nicholas Breen's avatar Nicholas Breen

* New upstream release.

* man/g_options.1: Create man page for new binary.
* lintian-overrides.gromacs-data: Override script-not-executable for demo scripts not in $PATH.
parent a84463bc
gromacs (4.5.3-2) UNRELEASED; urgency=low
gromacs (4.5.4-1) unstable; urgency=low
* New upstream release.
* Remove gromacs-lam transitional package.
* man/g_options.1: Create man page for new binary.
* lintian-overrides.gromacs-data: Override script-not-executable for demo
scripts not in $PATH.
-- Nicholas Breen <nbreen@ofb.net> Wed, 09 Feb 2011 09:22:14 -0800
-- Nicholas Breen <nbreen@ofb.net> Mon, 21 Mar 2011 19:59:54 -0700
gromacs (4.5.3-1) unstable; urgency=low
......
......@@ -105,6 +105,8 @@ gromacs: binary-without-manpage usr/bin/g_nmens
gromacs: binary-without-manpage usr/bin/g_nmens_d
gromacs: binary-without-manpage usr/bin/g_nmtraj
gromacs: binary-without-manpage usr/bin/g_nmtraj_d
gromacs: binary-without-manpage usr/bin/g_options
gromacs: binary-without-manpage usr/bin/g_options_d
gromacs: binary-without-manpage usr/bin/g_order
gromacs: binary-without-manpage usr/bin/g_order_d
gromacs: binary-without-manpage usr/bin/g_polystat
......
gromacs-data: csh-considered-harmful
gromacs-data: debhelper-but-no-misc-depends
# demo scripts
gromacs-data: script-not-executable
.TH g_options 1 "Mon 21 Mar 2011" "" "GROMACS suite, VERSION 4.5.4"
.SH NAME
g_options
.B VERSION 4.5.4
.SH SYNOPSIS
\f3g_options\fP
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.SH DESCRIPTION
\&GROMACS programs have some standard options,
\&of which some are hidden by default:
.SH OTHER OPTIONS
.BI "\-[no]h" "no "
Print help info and quit
.BI "\-[no]version" "no "
Print version info and quit
.BI "\-nice" " int" " 0"
Set the nicelevel
.SH KNOWN PROBLEMS
\- If the configuration script found Motif or Lesstif on your system, you can use the graphical interface (if not, you will get an error):
\fB \-X\fR gmx_bool \fB no\fR Use dialog box GUI to edit command line options
\- When compiled on an SGI\-IRIX system, all GROMACS programs have an additional option:
\fB \-npri\fR int \fB 0\fR Set non blocking priority (try 128)
\- Optional files are not used unless the option is set, in contrast to non\-optional files, where the default file name is used when the option is not set.
\- All GROMACS programs will accept file options without a file extension or filename being specified. In such cases the default filenames will be used. With multiple input file types, such as generic structure format, the directory will be searched for files of each type with the supplied or default name. When no such file is found, or with output files the first file type will be used.
\- All GROMACS programs with the exception of \fB mdrun\fR and \fB eneconv\fR check if the command line options are valid. If this is not the case, the program will be halted.
\- Enumerated options (enum) should be used with one of the arguments listed in the option description, the argument may be abbreviated. The first match to the shortest argument in the list will be selected.
\- Vector options can be used with 1 or 3 parameters. When only one parameter is supplied the two others are also set to this value.
\- All GROMACS programs can read compressed or g\-zipped files. There might be a problem with reading compressed \fB .xtc\fR, \fB .trr\fR and \fB .trj\fR files, but these will not compress very well anyway.
\- Most GROMACS programs can process a trajectory with fewer atoms than the run input or structure file, but only if the trajectory consists of the first n atoms of the run input or structure file.
\- Many GROMACS programs will accept the \fB \-tu\fR option to set the time units to use in output files (e.g. for \fB xmgr\fR graphs or \fB xpm\fR matrices) and in all time options.
.SH SEE ALSO
.BR gromacs(7)
More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
......@@ -173,7 +173,7 @@ 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/g_luck.1 debian/man/g_kinetics.1
dh_installman -pgromacs debian/man/g_luck.1 debian/man/g_kinetics.1 debian/man/g_options.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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