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gmx-velacc - Online in the Cloud

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This is the command gmx-velacc that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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

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