table of contents
g_rmsdist(1) | GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c | g_rmsdist(1) |
NAME¶
g_rmsdist - calculates atom pair distances averaged with power -2, -3 or -6SYNOPSIS¶
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]pbcDESCRIPTION¶
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.FILES¶
-f traj.xtc InputTrajectory: xtc trr trj gro g96 pdb cpt
Structure+mass(db): tpr tpb tpa gro g96 pdb
Index file
Generic data file
xvgr/xmgr file
X PixMap compatible matrix file
X PixMap compatible matrix file
X PixMap compatible matrix file
X PixMap compatible matrix file
X PixMap compatible matrix file
Generic data file
OTHER OPTIONS¶
-[no]hnoPrint help info and quit
Print version info and quit
Set the nicelevel
First frame (ps) to read from trajectory
Last frame (ps) to read from trajectory
Only use frame when t MOD dt = first time (ps)
View output .xvg, .xpm, .eps and .pdb files
xvg plot formatting: xmgrace, xmgr or none
Discretize rms in levels
Maximum level in matrices
average distance over equivalent hydrogens
Use periodic boundary conditions when computing distances
SEE ALSO¶
gromacs(7)Mon 4 Apr 2011 |