NAME
g_disre - analyzes distance restraints
VERSION 4.0.1
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 -x matrix.xpm -[no]h -nice int -b time -e time
-dt time -[no]w -[no]xvgr -ntop int -maxdr real -nlevels int -[no]third
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 always 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 third power averaging
algorithm and print them in the log file.
FILES
-s topol.tpr Input
Run input file: tpr tpb tpa
-f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt
-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
-x matrix.xpm Output, Opt.
X PixMap compatible matrix file
OTHER OPTIONS
-[no]hno
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]wno
View output xvg, xpm, eps and pdb files
-[no]xvgryes
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
-maxdr real 0
Maximum distance violation in matrix output. If less than or equal to
0 the maximum will be determined by the data.
-nlevels int 20
Number of levels in the matrix output
-[no]thirdyes
Use inverse third power averaging or linear for matrix output
SEE ALSO
gromacs(7)
More information about GROMACS is available at
<http://www.gromacs.org/>.
Thu 16 Oct 2008 g_disre(1)