NAME¶

g_vanhove - calculates Van Hove displacement functions VERSION 4.5.4-dev-20110404-bc5695c

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 -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -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 -[no]versionno
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]wno
View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none -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

SEE ALSO¶

gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>.