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GMX-VELACC(1)			    GROMACS			 GMX-VELACC(1)

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 autocor-
       relation	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/^a|>] (traj.trr)
	      Full precision trajectory: trr cpt tng

       -s [<.tpr/.gro/^a|>] (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 func-
	      tion

       -endfit <real> (-1)
	      Time  where  to end the exponential fit of the correlation func-
	      tion, -1 is until	the end

SEE ALSO
       gmx(1)

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

COPYRIGHT
       2020, GROMACS development team

2020.3				 Jul 09, 2020			 GMX-VELACC(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT

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