NAME

       gmx-velacc - Calculate velocity autocorrelation functions

SYNOPSIS

          gmx velacc [-f [<.trr/.cpt/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
                     [-o [<.xvg>]] [-os [<.xvg>]] [-b <time>] [-e <time>]
                     [-dt <time>] [-[no]w] [-xvg <enum>] [-[no]m] [-[no]recip]
                     [-[no]mol] [-acflen <int>] [-[no]normalize] [-P <enum>]
                     [-fitfn <enum>] [-beginfit <real>] [-endfit <real>]

DESCRIPTION

       gmx  velacc  computes  the velocity autocorrelation function.  When the -m option is used,
       the momentum autocorrelation function is calculated.

       With option -mol the velocity autocorrelation function of molecules is calculated. In this
       case the index group should consist of molecule numbers instead of atom numbers.

       Be  sure  that your trajectory contains frames with velocity information (i.e. nstvout was
       set in your original .mdp file), and that the time interval between data collection points
       is much shorter than the time scale of the autocorrelation.

OPTIONS

       Options to specify input files:

       -f [<.trr/.cpt/...>] (traj.trr)
              Full precision trajectory: trr cpt tng

       -s [<.tpr/.gro/...>] (topol.tpr) (Optional)
              Structure+mass(db): tpr gro g96 pdb brk ent

       -n [<.ndx>] (index.ndx) (Optional)
              Index file

       Options to specify output files:

       -o [<.xvg>] (vac.xvg)
              xvgr/xmgr file

       -os [<.xvg>] (spectrum.xvg) (Optional)
              xvgr/xmgr file

       Other options:

       -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]w (no)
              View output .xvg, .xpm, .eps and .pdb files

       -xvg <enum>
              xvg plot formatting: xmgrace, xmgr, none

       -[no]m (no)
              Calculate the momentum autocorrelation function

       -[no]recip (yes)
              Use cm^-1 on X-axis instead of 1/ps for spectra.

       -[no]mol (no)
              Calculate the velocity acf of molecules

       -acflen <int> (-1)
              Length of the ACF, default is half the number of frames

       -[no]normalize (yes)
              Normalize ACF

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

       -fitfn <enum> (none)
              Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9

       -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

SEE ALSO

       gmx(1)

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

COPYRIGHT

       2015, GROMACS development team