Man page - gmx-vanhove(1)
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apt-get install gromacs-data
Manual
GMX-VANHOVE
NAMESYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO
COPYRIGHT
NAME
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)
Time of first frame to read from trajectory (default unit ps)
-e <time> (0)
Time of last frame to read from trajectory (default unit ps)
-dt <time> (0)
Only use frame when t MOD dt = first time (default unit 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
gmx(1)
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2025, GROMACS development team