g_velacc (1) - Linux Manuals

g_velacc: calculates velocity autocorrelation functions

NAME

g_velacc - calculates velocity autocorrelation functions

VERSION 4.0.1

SYNOPSIS

g_velacc -f traj.trr -s topol.tpr -n index.ndx -o vac.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]m -[no]mol -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real

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.

FILES

-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 

OTHER OPTIONS

-[no]hno
 Print help 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]wno
 View output xvg, xpm, eps and pdb files

-[no]xvgryes
 Add specific codes (legends etc.) in the output xvg files for the xmgrace program

-[no]mno
 Calculate the momentum autocorrelation function

-[no]molno
 Calculate the velocity acf of molecules

-acflen int -1
 Length of the ACF, default is half the number of frames

-[no]normalizeyes
 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 or  exp9

-ncskip int 0
 Skip N 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 till the end