.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>.