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/>.