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PROGRAM:

NAME


gmx-rms - Calculate RMSDs with a reference structure and RMSD matrices

SYNOPSIS


gmx rms [-s [<.tpr/.gro/...>]] [-f [<.xtc/.trr/...>]]
[-f2 [<.xtc/.trr/...>]] [-n [<.ndx>]] [-o [<.xvg>]]
[-mir [<.xvg>]] [-a [<.xvg>]] [-dist [<.xvg>]] [-m [<.xpm>]]
[-bin [<.dat>]] [-bm [<.xpm>]] [-b <time>] [-e <time>]
[-dt <time>] [-tu <enum>] [-[no]w] [-xvg <enum>]
[-what <enum>] [-[no]pbc] [-fit <enum>] [-prev <int>]
[-[no]split] [-skip <int>] [-skip2 <int>] [-max <real>]
[-min <real>] [-bmax <real>] [-bmin <real>] [-[no]mw]
[-nlevels <int>] [-ng <int>]

DESCRIPTION


gmx rms compares two structures by computing the root mean square deviation (RMSD), the
size-independent rho similarity parameter (rho) or the scaled rho (rhosc), see Maiorov &
Crippen, Proteins 22, 273 (1995). This is selected by -what.

Each structure from a trajectory (-f) is compared to a reference structure. The reference
structure is taken from the structure file (-s).

With option -mir also a comparison with the mirror image of the reference structure is
calculated. This is useful as a reference for 'significant' values, see Maiorov &
Crippen, Proteins 22, 273 (1995).

Option -prev produces the comparison with a previous frame the specified number of frames
ago.

Option -m produces a matrix in .xpm format of comparison values of each structure in the
trajectory with respect to each other structure. This file can be visualized with for
instance xv and can be converted to postscript with gmx xpm2ps.

Option -fit controls the least-squares fitting of the structures on top of each other:
complete fit (rotation and translation), translation only, or no fitting at all.

Option -mw controls whether mass weighting is done or not. If you select the option
(default) and supply a valid .tpr file masses will be taken from there, otherwise the
masses will be deduced from the atommass.dat file in GMXLIB. This is fine for proteins,
but not necessarily for other molecules. A default mass of 12.011 amu (carbon) is assigned
to unknown atoms. You can check whether this happened by turning on the -debug flag and
inspecting the log file.

With -f2, the 'other structures' are taken from a second trajectory, this generates a
comparison matrix of one trajectory versus the other.

Option -bin does a binary dump of the comparison matrix.

Option -bm produces a matrix of average bond angle deviations analogously to the -m
option. Only bonds between atoms in the comparison group are considered.

OPTIONS


Options to specify input files:

-s [<.tpr/.gro/...>] (topol.tpr)
Structure+mass(db): tpr gro g96 pdb brk ent

-f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng

-f2 [<.xtc/.trr/...>] (traj.xtc) (Optional)
Trajectory: xtc trr cpt gro g96 pdb tng

-n [<.ndx>] (index.ndx) (Optional)
Index file

Options to specify output files:

-o [<.xvg>] (rmsd.xvg)
xvgr/xmgr file

-mir [<.xvg>] (rmsdmir.xvg) (Optional)
xvgr/xmgr file

-a [<.xvg>] (avgrp.xvg) (Optional)
xvgr/xmgr file

-dist [<.xvg>] (rmsd-dist.xvg) (Optional)
xvgr/xmgr file

-m [<.xpm>] (rmsd.xpm) (Optional)
X PixMap compatible matrix file

-bin [<.dat>] (rmsd.dat) (Optional)
Generic data file

-bm [<.xpm>] (bond.xpm) (Optional)
X PixMap compatible matrix file

Other options:

-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)

-tu <enum> (ps)
Unit for time values: fs, ps, ns, us, ms, s

-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files

-xvg <enum>
xvg plot formatting: xmgrace, xmgr, none

-what <enum> (rmsd)
Structural difference measure: rmsd, rho, rhosc

-[no]pbc (yes)
PBC check

-fit <enum> (rot+trans)
Fit to reference structure: rot+trans, translation, none

-prev <int> (0)
Compare with previous frame

-[no]split (no)
Split graph where time is zero

-skip <int> (1)
Only write every nr-th frame to matrix

-skip2 <int> (1)
Only write every nr-th frame to matrix

-max <real> (-1)
Maximum level in comparison matrix

-min <real> (-1)
Minimum level in comparison matrix

-bmax <real> (-1)
Maximum level in bond angle matrix

-bmin <real> (-1)
Minimum level in bond angle matrix

-[no]mw (yes)
Use mass weighting for superposition

-nlevels <int> (80)
Number of levels in the matrices

-ng <int> (1)
Number of groups to compute RMS between

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