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)