GMX-RMS(1)

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)
    Time of first frame to read from trajectory (default unit ps)

-e <time> (0)
    Time of last frame to read from trajectory (default unit ps)

-dt <time> (0)
    Only use frame when t MOD dt = first time (default unit 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> (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 ALSO

gmx(1)

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