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g_vanhove(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				      g_vanhove(1)

NAME
g_vanhove - calculates Van Hove displacement functions VERSION 4.5.4-dev-20110404-bc5695c 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 -[no]version -nice int -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
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 probabil- ity 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 -[no]versionno 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) -[no]wno 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 SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_vanhove(1)

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g_mindist(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				      g_mindist(1)

NAME
g_mindist - calculates the minimum distance between two groups VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_mindist -f traj.xtc -s topol.tpr -n index.ndx -od mindist.xvg -on numcont.xvg -o atm-pair.out -ox mindist.xtc -or mindistres.xvg -[no]h -[no]version -nice int -b time -e time -dt time -tu enum -[no]w -xvg enum -[no]matrix -[no]max -d real -[no]group -[no]pi -[no]split -ng int -[no]pbc -[no]respertime -[no]printresname DESCRIPTION
g_mindist computes the distance between one group and a number of other groups. Both the minimum distance (between any pair of atoms from the respective groups) and the number of contacts within a given distance are written to two separate output files. With the -group option a contact of an atom in other group with multiple atoms in the first group is counted as one contact instead of as multiple con- tacts. With -or, minimum distances to each residue in the first group are determined and plotted as a function of residue number. With option -pi the minimum distance of a group to its periodic image is plotted. This is useful for checking if a protein has seen its periodic image during a simulation. Only one shift in each direction is considered, giving a total of 26 shifts. It also plots the maximum distance within the group and the lengths of the three box vectors. Other programs that calculate distances are g_dist and g_bond. FILES
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -s topol.tpr Input, Opt. Structure+mass(db): tpr tpb tpa gro g96 pdb -n index.ndx Input, Opt. Index file -od mindist.xvg Output xvgr/xmgr file -on numcont.xvg Output, Opt. xvgr/xmgr file -o atm-pair.out Output, Opt. Generic output file -ox mindist.xtc Output, Opt. Trajectory: xtc trr trj gro g96 pdb -or mindistres.xvg Output, Opt. xvgr/xmgr file OTHER OPTIONS
-[no]hno Print help info and quit -[no]versionno 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) -tu enum ps Time unit: fs, ps, ns, us, ms or s -[no]wno View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -[no]matrixno Calculate half a matrix of group-group distances -[no]maxno Calculate *maximum* distance instead of minimum -d real 0.6 Distance for contacts -[no]groupno Count contacts with multiple atoms in the first group as one -[no]pino Calculate minimum distance with periodic images -[no]splitno Split graph where time is zero -ng int 1 Number of secondary groups to compute distance to a central group -[no]pbcyes Take periodic boundary conditions into account -[no]respertimeno When writing per-residue distances, write distance for each time point -[no]printresnameno Write residue names SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_mindist(1)
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