# g_vanhove(1) [debian man page]

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-bc5695cSYNOPSIS

g_vanhovetraj.xtc-ftopol.tpr-sindex.ndx-nvanhove.xpm-omvanhove_r.xvg-orvanhove_t.xvg -[no]h -[no]version-otint-nicetime-btime-etime -[no]w-dtenum-xvgreal-sqrtint-fmreal-rmaxreal-rbinreal-mmaxint-nlevelsint-nrint-frreal-rtint-ftDESCRIPTION

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 optionthe 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-omthe Van Hove function is plotted for one or more values of t. Option-orsets the number of times, option-nrthe number spacing between the times. The binwidth is set with option-frThe number of bins is determined automatically. With option-rbin.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-otand-omthe program may be slow. This is because the calculation scales as the number of frames times-otor-fmNote that with the-ft.option the memory usage and calculation time can be reduced.-dtFILES

traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt-ftopol.tpr Input Structure+mass(db): tpr tpb tpa gro g96 pdb-sindex.ndx Input, Opt. Index file-nvanhove.xpm Output, Opt. X PixMap compatible matrix file-omvanhove_r.xvg Output, Opt. xvgr/xmgr file-orvanhove_t.xvg Output, Opt. xvgr/xmgr file-otOTHER OPTIONS

-[no]hno Print help info and quit -[no]versionno Print version info and quitint 19 Set the nicelevel-nicetime 0 First frame (ps) to read from trajectory-btime 0 Last frame (ps) to read from trajectory-etime 0 Only use frame when t MOD dt = first time (ps) -[no]wno View output .xvg, .xpm, .eps and .pdb files-dtenum xmgrace xvg plot formatting: xmgrace, xmgr or none-xvgreal 0 Use sqrt(t) on the matrix axis which binspacing in sqrt(ps)-sqrtint 0 Number of frames in the matrix, 0 is plot all-fmreal 2 Maximum r in the matrix (nm)-rmaxreal 0.01 Binwidth in the matrix and for-rbin(nm)-orreal 0 Maximum density in the matrix, 0 is calculate (1/nm)-mmaxint 81 Number of levels in the matrix-nlevelsint 1 Number of curves for the-nroutput-orint 0 Frame spacing for the-froutput-orreal 0 Integration limit for the-rtoutput (nm)-otint 0 Number of frames in the-ftoutput, 0 is plot all-otSEE 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-bc5695cSYNOPSIS

g_mindisttraj.xtc-ftopol.tpr-sindex.ndx-nmindist.xvg-odnumcont.xvg-onatm-pair.out-omindist.xtc-oxmindistres.xvg -[no]h -[no]version-orint-nicetime-btime-etime-dtenum -[no]w-tuenum -[no]matrix -[no]max-xvgreal -[no]group -[no]pi -[no]split-dint -[no]pbc -[no]respertime -[no]printresname-ngDESCRIPTION

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 theoption 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-group, minimum distances to each residue in the first group are determined and plotted as a function of residue number. With option-orthe 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.-piFILES

traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt-ftopol.tpr Input, Opt. Structure+mass(db): tpr tpb tpa gro g96 pdb-sindex.ndx Input, Opt. Index file-nmindist.xvg Output xvgr/xmgr file-odnumcont.xvg Output, Opt. xvgr/xmgr file-onatm-pair.out Output, Opt. Generic output file-omindist.xtc Output, Opt. Trajectory: xtc trr trj gro g96 pdb-oxmindistres.xvg Output, Opt. xvgr/xmgr file-orOTHER OPTIONS

-[no]hno Print help info and quit -[no]versionno Print version info and quitint 19 Set the nicelevel-nicetime 0 First frame (ps) to read from trajectory-btime 0 Last frame (ps) to read from trajectory-etime 0 Only use frame when t MOD dt = first time (ps)-dtenum ps Time unit: fs, ps, ns, us, ms or s -[no]wno View output .xvg, .xpm, .eps and .pdb files-tuenum 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-xvgreal 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-dint 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-ngSEE ALSO

gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_mindist(1)