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.

       By using option -os you can also extract the estimated (vibrational) power spectrum, which is the Fourier
       transform of the velocity autocorrelation function.  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)
              Time of first frame to read from trajectory (default unit ps)

       -e <time> (0)
              Time of last frame to read from trajectory (default unit ps)

       -dt <time> (0)
              Only use frame when t MOD dt = first time (default unit ps)

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

       -xvg <enum> (xmgrace)
              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

       2023, GROMACS development team

2023.3                                            Oct 19, 2023                                     GMX-VELACC(1)