Commit 4fed5f5b authored by Nicholas Breen's avatar Nicholas Breen

man/g_dos.1: Create man page for new binary.

parent 6b42afb1
gromacs (4.5.5-1) UNRELEASED; urgency=low
gromacs (4.5.5-1) unstable; urgency=low
* New upstream release.
- Remove patches/30_git_release-4.5-patches.dpatch.
- man/g_dos.1: Create man page for new binary.
* rules: Add build-arch/build-indep targets. Add preliminary support for
building GPU-accelerated binaries: set DEB_BUILD_OPTIONS=gpu to try it.
-- Nicholas Breen <nbreen@ofb.net> Mon, 19 Sep 2011 14:49:41 -0700
-- Nicholas Breen <nbreen@ofb.net> Wed, 21 Sep 2011 15:26:14 -0700
gromacs (4.5.4-2) unstable; urgency=low
......
.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>.
......@@ -180,7 +180,7 @@ 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 debian/man/g_options.1
dh_installman -pgromacs debian/man/g_*.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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