g_disre

NAME

g_disre − analyzes distance restraints

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