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GMX-RMS(1) GROMACS 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 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 se- lect 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 (deprecated). This is fine for proteins, but not necessarily for other molecules. You can check whether this hap- pened 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 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) More information about GROMACS is available at <- http://www.gromacs.org/>. COPYRIGHT 2025, GROMACS development team 2025.0 Feb 10, 2025 GMX-RMS(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT
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