g_mindist

Main Table of Contents

VERSION 3.2.0
Sun 25 Jan 2004


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 -or, minimum distances to each residue in the first group are determined and plotted as a function of reisdue 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

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 xml
-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. Generic trajectory: xtc trr trj gro g96 pdb
-or mindistres.xvg Output, Opt. xvgr/xmgr file

Other options

optiontypedefaultdescription
-[no]h bool no Print help info and quit
-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)
-tu enum ps Time unit: ps, fs, ns, us, ms, s, m or h
-[no]w bool no View output xvg, xpm, eps and pdb files
-[no]matrix bool no Calculate half a matrix of group-group distances
-[no]max bool no Calculate *maximum* distance instead of minimum
-d real 0.6 Distance for contacts
-[no]pi bool no Calculate minimum distance with periodic images
-[no]split bool no Split graph where time is zero


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