.TH g_mindist 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
g_mindist - calculates the minimum distance between two groups

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3g_mindist\fP
.BI "\-f" " traj.xtc "
.BI "\-s" " topol.tpr "
.BI "\-n" " index.ndx "
.BI "\-od" " mindist.xvg "
.BI "\-on" " numcont.xvg "
.BI "\-o" " atm\-pair.out "
.BI "\-ox" " mindist.xtc "
.BI "\-or" " mindistres.xvg "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-tu" " enum "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-[no]matrix" ""
.BI "\-[no]max" ""
.BI "\-d" " real "
.BI "\-[no]group" ""
.BI "\-[no]pi" ""
.BI "\-[no]split" ""
.BI "\-ng" " int "
.BI "\-[no]pbc" ""
.BI "\-[no]respertime" ""
.BI "\-[no]printresname" ""
.SH DESCRIPTION
\&\fB g_mindist\fR 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 \fB \-group\fR 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 contacts.
\&With \fB \-or\fR, minimum distances to each residue in the first
\&group are determined and plotted as a function of residue number.


\&With option \fB \-pi\fR 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 \fB g_dist\fR
\&and \fB g_bond\fR.
.SH FILES
.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-s" " topol.tpr" 
.B Input, Opt.
 Structure+mass(db): tpr tpb tpa gro g96 pdb 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-od" " mindist.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-on" " numcont.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-o" " atm\-pair.out" 
.B Output, Opt.
 Generic output file 

.BI "\-ox" " mindist.xtc" 
.B Output, Opt.
 Trajectory: xtc trr trj gro g96 pdb 

.BI "\-or" " mindistres.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-tu"  " enum" " ps" 
 Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR

.BI "\-[no]w"  "no    "
 View output \fB .xvg\fR, \fB .xpm\fR, \fB .eps\fR and \fB .pdb\fR files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-[no]matrix"  "no    "
 Calculate half a matrix of group\-group distances

.BI "\-[no]max"  "no    "
 Calculate *maximum* distance instead of minimum

.BI "\-d"  " real" " 0.6   " 
 Distance for contacts

.BI "\-[no]group"  "no    "
 Count contacts with multiple atoms in the first group as one

.BI "\-[no]pi"  "no    "
 Calculate minimum distance with periodic images

.BI "\-[no]split"  "no    "
 Split graph where time is zero

.BI "\-ng"  " int" " 1" 
 Number of secondary groups to compute distance to a central group

.BI "\-[no]pbc"  "yes   "
 Take periodic boundary conditions into account

.BI "\-[no]respertime"  "no    "
 When writing per\-residue distances, write distance for each time point

.BI "\-[no]printresname"  "no    "
 Write residue names

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.