Provided by: gromacs-data_2018.1-1_all bug


       gmx-velacc - Calculate velocity autocorrelation functions


          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>]


       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 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



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       2018, GROMACS development team