xenial (1) gmx-velacc.1.gz

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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/>.

       2015, GROMACS development team