g_rmsdist(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_rmsdist(1)
NAME
g_rmsdist - calculates atom pair distances averaged with power -2, -3 or -6
VERSION 4.5.4-dev-20110404-bc5695c
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 -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -nlevels int -max real
-[no]sumh -[no]pbc
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
-[no]versionno
Print version 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
-xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none
-nlevels int 40
Discretize rms in levels
-max real -1
Maximum level in matrices
-[no]sumhyes
average distance over equivalent hydrogens
-[no]pbcyes
Use periodic boundary conditions when computing distances
SEE ALSO
gromacs(7)
More information about GROMACS is available at <http://www.gromacs.org/>.
Mon 4 Apr 2011 g_rmsdist(1)