Main Table of Contents

Fri 5 Jul 2013


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/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.:


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

Other options

-[no]h bool no Print help info and quit
-[no]version bool no 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]w bool no 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]sumh bool yes Average distance over equivalent hydrogens
-[no]pbc bool yes Use periodic boundary conditions when computing distances