g_velacc

Main Table of Contents

VERSION 4.6.5
Mon 2 Dec 2013


Description

g_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.

Files

optionfilenametypedescription
-f traj.trr Input Full precision trajectory: trr trj cpt
-s topol.tpr Input, Opt. Structure+mass(db): tpr tpb tpa gro g96 pdb
-n index.ndx Input, Opt. Index file
-o vac.xvg Output xvgr/xmgr file
-os spectrum.xvg Output, Opt. xvgr/xmgr file

Other options

optiontypedefaultdescription
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 19 Set the nicelevel
-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 bool no View output .xvg, .xpm, .eps and .pdb files
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-[no]m bool no Calculate the momentum autocorrelation function
-[no]recip bool yes Use cm^-1 on X-axis instead of 1/ps for spectra.
-[no]mol bool no Calculate the velocity acf of molecules
-acflen int -1 Length of the ACF, default is half the number of frames
-[no]normalize bool yes Normalize ACF
-P enum 0 Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3
-fitfn enum none Fit function: none, exp, aexp, exp_exp, vac, exp5, exp7, exp9 or erffit
-ncskip int 0 Skip this many points in the output file of correlation functions
-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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