gmx vanhove¶
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