g_rmsdist(1)
NAME
g_rmsdist - calculates atom pair distances averaged with power 2, -3 or
-6
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
- Generic 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 no
- 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]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
SEE ALSO
- More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.