.TH genrestr 1 "Mon 4 Apr 2011" "" "GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c"
.SH NAME
genrestr - generates position restraints or distance restraints for index groups

.B VERSION 4.5.4-dev-20110404-bc5695c
.SH SYNOPSIS
\f3genrestr\fP
.BI "\-f" " conf.gro "
.BI "\-n" " index.ndx "
.BI "\-o" " posre.itp "
.BI "\-of" " freeze.ndx "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-fc" " vector "
.BI "\-freeze" " real "
.BI "\-[no]disre" ""
.BI "\-disre_dist" " real "
.BI "\-disre_frac" " real "
.BI "\-disre_up2" " real "
.BI "\-cutoff" " real "
.BI "\-[no]constr" ""
.SH DESCRIPTION
\&\fB genrestr\fR produces an include file for a topology containing
\&a list of atom numbers and three force constants for the
\&\fI x\fR\-, \fI y\fR\-, and \fI z\fR\-direction. A single isotropic force constant may
\&be given on the command line instead of three components.


\&WARNING: position restraints only work for the one molecule at a time.
\&Position restraints are interactions within molecules, therefore
\&they should be included within the correct \fB [ moleculetype ]\fR
\&block in the topology. Since the atom numbers in every moleculetype
\&in the topology start at 1 and the numbers in the input file for
\&\fB genrestr\fR number consecutively from 1, \fB genrestr\fR will only
\&produce a useful file for the first molecule.


\&The \fB \-of\fR option produces an index file that can be used for
\&freezing atoms. In this case, the input file must be a \fB .pdb\fR file.


\&With the \fB \-disre\fR option, half a matrix of distance restraints
\&is generated instead of position restraints. With this matrix, that
\&one typically would apply to Calpha atoms in a protein, one can
\&maintain the overall conformation of a protein without tieing it to
\&a specific position (as with position restraints).
.SH FILES
.BI "\-f" " conf.gro" 
.B Input
 Structure file: gro g96 pdb tpr etc. 

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

.BI "\-o" " posre.itp" 
.B Output
 Include file for topology 

.BI "\-of" " freeze.ndx" 
.B Output, Opt.
 Index 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" " 0" 
 Set the nicelevel

.BI "\-fc"  " vector" " 1000 1000 1000" 
 force constants (kJ/mol nm2)

.BI "\-freeze"  " real" " 0     " 
 if the \fB \-of\fR option or this one is given an index file will be written containing atom numbers of all atoms that have a B\-factor less than the level given here

.BI "\-[no]disre"  "no    "
 Generate a distance restraint matrix for all the atoms in index

.BI "\-disre_dist"  " real" " 0.1   " 
 Distance range around the actual distance for generating distance restraints

.BI "\-disre_frac"  " real" " 0     " 
 Fraction of distance to be used as interval rather than a fixed distance. If the fraction of the distance that you specify here is less than the distance given in the previous option, that one is used instead.

.BI "\-disre_up2"  " real" " 1     " 
 Distance between upper bound for distance restraints, and the distance at which the force becomes constant (see manual)

.BI "\-cutoff"  " real" " \-1    " 
 Only generate distance restraints for atoms pairs within cutoff (nm)

.BI "\-[no]constr"  "no    "
 Generate a constraint matrix rather than distance restraints. Constraints of type 2 will be generated that do generate exclusions.

.SH SEE ALSO
.BR gromacs(7)

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