g_rmsdist_d (1) - Linux Man Pages

g_rmsdist_d: calculates atom pair distances averaged with power 2, -3 or -6

NAME

g_rmsdist - calculates atom pair distances averaged with power 2, -3 or -6

VERSION 4.0.1

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 -nice int -b time -e time -dt time -[no]w -[no]xvgr -nlevels int -max real -[no]sumh

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

-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

-[no]xvgryes
 Add specific codes (legends etc.) in the output xvg files for the xmgrace program

-nlevels int 40
 Discretize rms in  levels

-max real -1
 Maximum level in matrices

-[no]sumhyes
 average distance over equivalent hydrogens

SEE ALSO

gromacs(7)

More information about GROMACS is available at <http://www.gromacs.org/>.