g_rmsdist(1) - Linux man page

Name

g_rmsdist - calculates atom pair distances averaged with power -2, -3

or -6

VERSION 4.5.4-dev-20110404-bc5695c

Synopsis

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

Description

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.

Files

-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]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 levels

-max real -1 Maximum level in matrices

-[no]sumhyes average distance over equivalent hydrogens