g_rmsdist - calculates atom pair distances averaged with power -2, -3 or -6
VERSION 4.6.3
g_rmsdist −f traj.xtc −s topol.tpr −n index.ndx −equiv equiv.dat −o distrmsd.xvg −rms rmsdist.xpm −scl rmsscale.xpm −mean rmsmean.xpm −nmr3 nmr3.xpm −nmr6 nmr6.xpm −noe noe.dat −[no]h −[no]version −nice int −b time −e time −dt time −[no]w −xvg enum −nlevels int −max real −[no]sumh −[no]pbc
g_rmsdist computes the root mean square deviation of atom distances, which has the advantage that no fit is needed like in standard RMS deviation as computed by g_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.
g_rmsdist can also produce matrices of the rms distances, rms distances scaled with the mean distance and the mean distances and matrices with NMR averaged distances (1/r3 and 1/r6 averaging). Finally, lists of atom pairs with 1/r3 and 1/r6 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.:
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.
−f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt
−s topol.tpr Input
Structure+mass(db): tpr tpb tpa gro g96 pdb
−n index.ndx Input, Opt.
Index file
−equiv equiv.dat Input, Opt.
Generic data file
−o distrmsd.xvg Output
xvgr/xmgr file
−rms rmsdist.xpm Output, Opt.
X PixMap compatible matrix file
−scl rmsscale.xpm Output, Opt.
X PixMap compatible matrix file
−mean rmsmean.xpm Output, Opt.
X PixMap compatible matrix file
−nmr3 nmr3.xpm Output, Opt.
X PixMap compatible matrix file
−nmr6 nmr6.xpm Output, Opt.
X PixMap compatible matrix file
−noe noe.dat Output, Opt.
Generic data file
−[no]hno
Print help info and quit
−[no]versionno
Print version info and quit
−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)
−[no]wno
View output .xvg, .xpm, .eps and .pdb files
−xvg enum xmgrace
xvg plot formatting: xmgrace, xmgr or none
−nlevels int 40
Discretize RMS in this number of levels
−max real −1
Maximum level in matrices
−[no]sumhyes
Average distance over equivalent hydrogens
−[no]pbcyes
Use periodic boundary conditions when computing distances
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