man g_disre (Commandes) - g_disre VERSION 3.3_beta_20050823
NAME
g_disre VERSION 3.3_beta_20050823
SYNOPSIS
g_disre -s topol.tpr -f traj.xtc -ds drsum.xvg -da draver.xvg -dn drnum.xvg -dm drmax.xvg -dr restr.xvg -l disres.log -n viol.ndx -q viol.pdb -c clust.ndx -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -ntop int
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.
When the -c option is given, an index file will be read containing the frames in your trajectory corresponding to the clusters (defined in another manner) that you want to analyze. For these clusters the program will compute average violations using the thisd power averaging algorithm and print them in the log file.
FILES
-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
-c clust.ndx Input, Opt. Index file
OTHER OPTIONS
-[no]h no Print help info and quit
-nice int 19 Set the nicelevel
-b time 0 First frame (ps) to read from trajectory
-e time 0 Last frame (ps) to read from trajectory
-dt time 0 Only use frame when t MOD dt = first time (ps)
-[no]w no View output xvg, xpm, eps and pdb files
-[no]xvgr yes Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-ntop int 0 Number of large violations that are stored in the log file every step