NAME

       g_dos - compute density of states from a simulation trajectory VERSION 4.5.5

SYNOPSIS

       g_dos  -f  traj.trr -s topol.tpr -n index.ndx -vacf vacf.xvg -mvacf mvacf.xvg -dos dos.xvg
       -g dos.log -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum  -[no]v
       -[no]recip  -[no]abs  -[no]normdos  -T real -acflen int -[no]normalize -P enum -fitfn enum
       -ncskip int -beginfit real -endfit real

DESCRIPTION

        g_dos 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.

FILES

       -f traj.trr Input
        Full precision trajectory: trr trj cpt

       -s topol.tpr Input
        Run input file: tpr tpb tpa

       -n index.ndx Input, Opt.
        Index file

       -vacf vacf.xvg Output
        xvgr/xmgr file

       -mvacf mvacf.xvg Output
        xvgr/xmgr file

       -dos dos.xvg Output
        xvgr/xmgr file

       -g dos.log Output
        Log file

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        Print version info and quit

       -nice int 19
        Set the nicelevel

       -b time 0
        First frame (ps) to read from trajectory

       -e time 0
        Last frame (ps) to read from trajectory

       -dt time 0
        Only use frame when t MOD dt = first time (ps)

       -[no]wno
        View output  .xvg,  .xpm,  .eps and  .pdb files

       -xvg enum xmgrace
        xvg plot formatting:  xmgrace,  xmgr or  none

       -[no]vyes
        Be loud and noisy.

       -[no]recipno
        Use cm-1 on X-axis instead of 1/ps for DoS plots.

       -[no]absno
        Use  the  absolute  value  of the Fourier transform of the VACF as the Density of States.
       Default is to use the real component only

       -[no]normdosno
        Normalize the DoS such that it adds up  to  3N.  This  is  a  hack  that  should  not  be
       necessary.

       -T real 298.15
        Temperature in the simulation

       -acflen int -1
        Length of the ACF, default is half the number of frames

       -[no]normalizeyes
        Normalize ACF

       -P enum 0
        Order of Legendre polynomial for ACF (0 indicates none):  0,  1,  2 or  3

       -fitfn enum none
        Fit function:  none,  exp,  aexp,  exp_exp,  vac,  exp5,  exp7,  exp9 or  erffit

       -ncskip int 0
        Skip N points in the output file of correlation functions

       -beginfit real 0
        Time where to begin the exponential fit of the correlation function

       -endfit real -1
        Time where to end the exponential fit of the correlation function, -1 is until the end

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).

SEE ALSO

       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

                                         Wed 21 Sep 2011                                 g_dos(1)