g_vanhove(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_vanhove(1)
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 probabil-
ity 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/>.
Mon 4 Apr 2011 g_vanhove(1)