gmx-rms(1) GROMACS Manual gmx-rms(1)NAMEgmx-rms - Calculate RMSDs with a reference structure and RMSD matrices
SYNOPSIS
gmx rms [-s [<.tpr/.tpb/...>]] [-f [<.xtc/.trr/...>]]
[-f2 [<.xtc/.trr/...>]] [-n [<.ndx>]] [-o [<.xvg>]]
[-mir [<.xvg>]] [-a [<.xvg>]] [-dist [<.xvg>]] [-m [<.xpm>]]
[-bin [<.dat>]] [-bm [<.xpm>]] [-nice <int>] [-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 devi‐
ation (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 struc‐
ture. The reference structure is taken from the structure file (-s).
With option -mir also a comparison with the mirror image of the refer‐
ence structure is calculated. This is useful as a reference for 'sig‐
nificant' values, see Maiorov & Crippen, Proteins 22, 273 (1995).
Option -prev produces the comparison with a previous frame the speci‐
fied 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 atom‐
mass.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 happend 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 analo‐
gously to the -m option. Only bonds between atoms in the comparison
group are considered.
OPTIONS
Options to specify input and output files:
-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent
-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-f2 [<.xtc/.trr/...>] (traj.xtc) (Input, Optional)
Trajectory: xtc trr cpt trj gro g96 pdb tng
-n [<.ndx>] (index.ndx) (Input, Optional)
Index file
-o [<.xvg>] (rmsd.xvg) (Output)
xvgr/xmgr file
-mir [<.xvg>] (rmsdmir.xvg) (Output, Optional)
xvgr/xmgr file
-a [<.xvg>] (avgrp.xvg) (Output, Optional)
xvgr/xmgr file
-dist [<.xvg>] (rmsd-dist.xvg) (Output, Optional)
xvgr/xmgr file
-m [<.xpm>] (rmsd.xpm) (Output, Optional)
X PixMap compatible matrix file
-bin [<.dat>] (rmsd.dat) (Output, Optional)
Generic data file
-bm [<.xpm>] (bond.xpm) (Output, Optional)
X PixMap compatible matrix 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)
-tu <enum> (ps)
Time unit: fs, ps, ns, us, ms, s
-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files
-xvg <enum> (xmgrace)
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
SEE ALSOgromacs(7)
More information about GROMACS is available at <http://www.gro‐
macs.org/>.
VERSION 5.0.6gmx-rms(1)
