gmx-disre(1) GROMACS Manual gmx-disre(1)NAMEgmx-disre - Analyze distance restraints
SYNOPSIS
gmx disre [-s [<.tpr/.tpb/...>]] [-f [<.xtc/.trr/...>]]
[-ds [<.xvg>]] [-da [<.xvg>]] [-dn [<.xvg>]] [-dm [<.xvg>]]
[-dr [<.xvg>]] [-l [<.log>]] [-n [<.ndx>]] [-q [<.pdb>]]
[-c [<.ndx>]] [-x [<.xpm>]] [-nice <int>] [-b <time>]
[-e <time>] [-dt <time>] [-[no]w] [-xvg <enum>]
[-ntop <int>] [-maxdr <real>] [-nlevels <int>] [-[no]third]
DESCRIPTION
gmx disre computes violations of distance restraints. If necessary, all
protons can be added to a protein molecule using the gmx protonate pro‐
gram.
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 pro‐
gram will compute average violations using the third power averaging
algorithm and print them in the log file.
OPTIONS
Options to specify input and output files:
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Run input file: tpr tpb tpa
-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-ds [<.xvg>] (drsum.xvg) (Output)
xvgr/xmgr file
-da [<.xvg>] (draver.xvg) (Output)
xvgr/xmgr file
-dn [<.xvg>] (drnum.xvg) (Output)
xvgr/xmgr file
-dm [<.xvg>] (drmax.xvg) (Output)
xvgr/xmgr file
-dr [<.xvg>] (restr.xvg) (Output)
xvgr/xmgr file
-l [<.log>] (disres.log) (Output)
Log file
-n [<.ndx>] (viol.ndx) (Input, Optional)
Index file
-q [<.pdb>] (viol.pdb) (Output, Optional)
Protein data bank file
-c [<.ndx>] (clust.ndx) (Input, Optional)
Index file
-x [<.xpm>] (matrix.xpm) (Output, Optional)
X PixMap compatible matrix file
Other options:
-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
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-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]third (yes)
Use inverse third power averaging or linear for matrix output
SEE ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-disre(1)
