gmx-rmsdist(1) GROMACS Manual gmx-rmsdist(1)NAMEgmx-rmsdist - Calculate atom pair distances averaged with power -2, -3
or -6
SYNOPSIS
gmx rmsdist [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]]
[-n [<.ndx>]] [-equiv [<.dat>]] [-o [<.xvg>]]
[-rms [<.xpm>]] [-scl [<.xpm>]] [-mean [<.xpm>]]
[-nmr3 [<.xpm>]] [-nmr6 [<.xpm>]] [-noe [<.dat>]]
[-nice <int>] [-b <time>] [-e <time>] [-dt <time>]
[-[no]w] [-xvg <enum>] [-nlevels <int>] [-max <real>]
[-[no]sumh] [-[no]pbc]
DESCRIPTION
gmx 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 gmx 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.
gmx rmsdist can also produce matrices of the rms distances, rms dis‐
tances scaled with the mean distance and the mean distances and matri‐
ces 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 max‐
imum 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.:
HB* 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.
OPTIONS
Options to specify input and output files:
-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Input, Optional)
Index file
-equiv [<.dat>] (equiv.dat) (Input, Optional)
Generic data file
-o [<.xvg>] (distrmsd.xvg) (Output)
xvgr/xmgr file
-rms [<.xpm>] (rmsdist.xpm) (Output, Optional)
X PixMap compatible matrix file
-scl [<.xpm>] (rmsscale.xpm) (Output, Optional)
X PixMap compatible matrix file
-mean [<.xpm>] (rmsmean.xpm) (Output, Optional)
X PixMap compatible matrix file
-nmr3 [<.xpm>] (nmr3.xpm) (Output, Optional)
X PixMap compatible matrix file
-nmr6 [<.xpm>] (nmr6.xpm) (Output, Optional)
X PixMap compatible matrix file
-noe [<.dat>] (noe.dat) (Output, Optional)
Generic data file
Other options:
-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
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-nlevels <int> (40)
Discretize RMS in this number of levels
-max <real> (-1)
Maximum level in matrices
-[no]sumh (yes)
Average distance over equivalent hydrogens
-[no]pbc (yes)
Use periodic boundary conditions when computing distances
SEE ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-rmsdist(1)
