NAME
g_rmsdist - calculates atom pair distances averaged with power 2, -3 or
-6
VERSION 4.0.1
SYNOPSIS
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]sumh
DESCRIPTION
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 Input
Trajectory: xtc trr trj gro g96 pdb cpt
-s topol.tpr Input
Structure+mass(db): tpr tpb tpa gro g96 pdb
-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]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
-nlevels int 40
Discretize rms in levels
-max real -1
Maximum level in matrices
-[no]sumhyes
average distance over equivalent hydrogens
SEE ALSO
gromacs(7)
More information about GROMACS is available at
<http://www.gromacs.org/>.
Thu 16 Oct 2008 g_rmsdist(1)