g_mindist


Main Table of Contents

VERSION 3.0
Tue 24 Jul 2001


Description

g_mindist computes the distance between one group and a number of other groups. Both the minimum distance and the number of contacts within a given distance are written to two separate output files.

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. This option is very slow.

Files

optionfilenametypedescription
-f traj.xtc Input Generic trajectory: xtc trr trj gro g96 pdb
-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 xvgr/xmgr file
-o atm-pair.out Output Generic output file

Other options

optiontypedefaultdescription
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-nice int 19 Set the nicelevel
-b time -1 First frame (ps) to read from trajectory
-e time -1 Last frame (ps) to read from trajectory
-dt time -1 Only use frame when t MOD dt = first time (ps)
-[no]w bool no View output xvg, xpm, eps and pdb files
-[no]matrix bool no Calculate half a matrix of group-group distances
-d real 0.6 Distance for contacts
-[no]pi bool no Calculate minimum distance with periodic images


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