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g_rmsdist
Langue: en
Version: 111391 (mandriva - 01/05/08)
Section: 1 (Commandes utilisateur)
NAME
g_rmsdist VERSION 3.3_beta_20050823SYNOPSIS
g_rmsdist -f traj.xtc -s topol.tpr -n index.ndx -equiv equiv.dat -o distrmsd.xvg -rms rmsdist.xpm -scl rmsscale.xpm -mean rmsmean.xpm -nmr3 nmr3.xpm -nmr6 nmr6.xpm -noe noe.dat -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -nlevels int -max real -[no]sumhDESCRIPTION
g_rmsdist computes the root mean square deviation of atom distances, which has the advantage that no fit is needed like in standard RMS deviation as computed by g_rms. The reference structure is taken from the structure file. The rmsd at time t is calculated as the rms of the differences in distance between atom-pairs in the reference structure and the structure at time t.g_rmsdist can also produce matrices of the rms distances, rms distances scaled with the mean distance and the mean distances and matrices with NMR averaged distances (1/r3 and 1/r6 averaging). Finally, lists of atom pairs with 1/r3 and 1/r6 averaged distance below the maximum distance ( -max , which will default to 0.6 in this case) can be generated, by default averaging over equivalent hydrogens (all triplets of hydrogens named *[123]). Additionally a list of equivalent atoms can be supplied ( -equiv ), each line containing a set of equivalent atoms specified as residue number and name and atom name; e.g.:
3 SER HB1 3 SER HB2
Residue and atom names must exactly match those in the structure file, including case. Specifying non-sequential atoms is undefined.
FILES
-f traj.xtc InputGeneric trajectory: xtc trr trj gro g96 pdb
-s topol.tpr Input
Structure+mass(db): tpr tpb tpa gro g96 pdb xml
-n index.ndx Input, Opt.
Index file
-equiv equiv.dat Input, Opt.
Generic data file
-o distrmsd.xvg Output
xvgr/xmgr file
-rms rmsdist.xpm Output, Opt.
X PixMap compatible matrix file
-scl rmsscale.xpm Output, Opt.
X PixMap compatible matrix file
-mean rmsmean.xpm Output, Opt.
X PixMap compatible matrix file
-nmr3 nmr3.xpm Output, Opt.
X PixMap compatible matrix file
-nmr6 nmr6.xpm Output, Opt.
X PixMap compatible matrix file
-noe noe.dat Output, Opt.
Generic data file
OTHER OPTIONS
-[no]h noPrint 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
-nlevels int 40
Discretize rms in levels
-max real -1
Maximum level in matrices
-[no]sumh yes
average distance over equivalent hydrogens
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre