gmx-vanhove(1) GROMACS Manual gmx-vanhove(1)NAMEgmx-vanhove - Compute Van Hove displacement and correlation functions
SYNOPSIS
gmx vanhove [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]]
[-n [<.ndx>]] [-om [<.xpm>]] [-or [<.xvg>]]
[-ot [<.xvg>]] [-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
gmx vanhove computes the Van Hove correlation function. The Van Hove
G(r,t) is the probability that a particle that is at r_0 at time zero
can be found at position r_0+r at time t. gmx 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 peri‐
odic 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 spac‐
ing between the times. The binwidth is set with option -rbin. The num‐
ber 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.
OPTIONS
Options to specify input and output files:
-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Input, Optional)
Index file
-om [<.xpm>] (vanhove.xpm) (Output, Optional)
X PixMap compatible matrix file
-or [<.xvg>] (vanhove_r.xvg) (Output, Optional)
xvgr/xmgr file
-ot [<.xvg>] (vanhove_t.xvg) (Output, Optional)
xvgr/xmgr file
Other options:
-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 (no)
View output .xvg, .xpm, .eps and .pdb files
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, 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 ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-vanhove(1)
