g_vanhove(1)
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
SEE ALSO
- More information about GROMACS is available at <http://www.gromacs.org/>.