g_disre

Main Table of Contents

VERSION 3.2.0
Sun 25 Jan 2004


Description

g_disre computes violations of distance restraints. If necessary all protons can be added to a protein molecule using the protonate program.

The program allways computes the instantaneous violations rather than time-averaged, because this analysis is done from a trajectory file afterwards it does not make sense to use time averaging. However, the time averaged values per restraint are given in the log file.

An index file may be used to select specific restraints for printing.

When the optional-q flag is given a pdb file coloured by the amount of average violations.

Files

optionfilenametypedescription
-s topol.tpr Input Generic run input: tpr tpb tpa xml
-f traj.xtc Input Generic trajectory: xtc trr trj gro g96 pdb
-ds drsum.xvg Output xvgr/xmgr file
-da draver.xvg Output xvgr/xmgr file
-dn drnum.xvg Output xvgr/xmgr file
-dm drmax.xvg Output xvgr/xmgr file
-dr restr.xvg Output xvgr/xmgr file
-l disres.log Output Log file
-n viol.ndx Input, Opt. Index file
-q viol.pdb Output, Opt. Protein data bank 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)
-[no]w bool no View output xvg, xpm, eps and pdb files
-ntop int 0 Number of large violations that are stored in the log file every step


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