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.
Structure+mass(db): tpr tpb tpa gro g96 pdb
X PixMap compatible matrix file
Print version 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)
View output xvg, xpm, eps and pdb files
-xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or 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
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