gmx-vanhove man page
gmx-vanhove — Compute Van Hove displacement and correlation functions
Synopsis
gmx vanhove [
-f [<.xtc/.trr/...>]] [
-s [<.tpr/.gro/...>]] [
-n [<.ndx>]] [
-om [<.xpm>]] [
-or [<.xvg>]] [
-ot [<.xvg>]] [
-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 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.
Options
Options to specify input files:
- -f [<.xtc/.trr/…>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng
- -s [<.tpr/.gro/…>] (topol.tpr)
Structure+mass(db): tpr gro g96 pdb brk ent
- -n [<.ndx>] (index.ndx) (Optional)
Index file
Options to specify output files:
- -om [<.xpm>] (vanhove.xpm) (Optional)
X PixMap compatible matrix file
- -or [<.xvg>] (vanhove_r.xvg) (Optional)
xvgr/xmgr file
- -ot [<.xvg>] (vanhove_t.xvg) (Optional)
xvgr/xmgr file
Other options:
- -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 Also
More information about GROMACS is available at <http://www.gromacs.org/>.
Copyright
2017, GROMACS development team