g_vanhove (1) - Linux Manuals

g_vanhove: calculates Van Hove displacement functions

NAME

g_vanhove - calculates Van Hove displacement functions

VERSION 4.0.1

SYNOPSIS

g_vanhove -f traj.xtc -s topol.tpr -n index.ndx -om vanhove.xpm -or vanhove_r.xvg -ot vanhove_t.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -sqrt real -fm int -rmax real -rbin real -mmax real -nlevels int -nr int -fr int -rt real -ft int

DESCRIPTION

g_vanhove computes the Van Hove correlation function. The Van Hove G(r,t) is the probability that a particle that is at r0 at time zero can be found at position r0+r at time t. g_vanhove determines G not for a vector r, but for the length of r. Thus it gives the probability that a particle moves a distance of r in time t. Jumps across the periodic boundaries are removed. Corrections are made for scaling due to isotropic or anisotropic pressure coupling.

With option -om the whole matrix can be written as a function of t and r or as a function of sqrt(t) and r (option -sqrt).

With option -or the Van Hove function is plotted for one or more values of t. Option -nr sets the number of times, option -fr the number spacing between the times. The binwidth is set with option -rbin. The number of bins is determined automatically.

With option -ot the integral up to a certain distance (option -rt) is plotted as a function of time.

For all frames that are read the coordinates of the selected particles are stored in memory. Therefore the program may use a lot of memory. For options -om and -ot the program may be slow. This is because the calculation scales as the number of frames times -fm or -ft. Note that with the -dt option the memory usage and calculation time can be reduced.

FILES

-f traj.xtc Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

-s topol.tpr Input
 Structure+mass(db): tpr tpb tpa gro g96 pdb 

-n index.ndx Input, Opt.
 Index file 

-om vanhove.xpm Output, Opt.
 X PixMap compatible matrix file 

-or vanhove_r.xvg Output, Opt.
 xvgr/xmgr file 

-ot vanhove_t.xvg Output, Opt.
 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

-sqrt real 0
 Use sqrt(t) on the matrix axis which binspacing  in sqrt(ps)

-fm int 0
 Number of frames in the matrix, 0 is plot all

-rmax real 2
 Maximum r in the matrix (nm)

-rbin real 0.01
 Binwidth in the matrix and for -or (nm)

-mmax real 0
 Maximum density in the matrix, 0 is calculate (1/nm)

-nlevels int 81
 Number of levels in the matrix

-nr int 1
 Number of curves for the -or output

-fr int 0
 Frame spacing for the -or output

-rt real 0
 Integration limit for the -ot output (nm)

-ft int 0
 Number of frames in the -ot output, 0 is plot all