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GMX-RMSDIST(1) GROMACS GMX-RMSDIST(1) NAME gmx-rmsdist - Calculate atom pair distances averaged with power -2, -3 or -6 SYNOPSIS gmx rmsdist [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]] [-equiv [<.dat>]] [-o [<.xvg>]] [-rms [<.xpm>]] [-scl [<.xpm>]] [-mean [<.xpm>]] [-nmr3 [<.xpm>]] [-nmr6 [<.xpm>]] [-noe [<.dat>]] [-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 de- viation 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/r^3 and 1/r^6 averaging). Finally, lists of atom pairs with 1/r^3 and 1/r^6 averaged distance below the maximum 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 files: -f [<.xtc/.trr/...>] (traj.xtc) Trajectory: xtc trr cpt gro g96 pdb tng -s [<.tpr/.gro/...>] (topol.tpr) Structure+mass(db): tpr gro g96 pdb brk ent -n [<.ndx>] (index.ndx) (Optional) Index file -equiv [<.dat>] (equiv.dat) (Optional) Generic data file Options to specify output files: -o [<.xvg>] (distrmsd.xvg) xvgr/xmgr file -rms [<.xpm>] (rmsdist.xpm) (Optional) X PixMap compatible matrix file -scl [<.xpm>] (rmsscale.xpm) (Optional) X PixMap compatible matrix file -mean [<.xpm>] (rmsmean.xpm) (Optional) X PixMap compatible matrix file -nmr3 [<.xpm>] (nmr3.xpm) (Optional) X PixMap compatible matrix file -nmr6 [<.xpm>] (nmr6.xpm) (Optional) X PixMap compatible matrix file -noe [<.dat>] (noe.dat) (Optional) Generic data 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) -[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 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-RMSDIST(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT
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