[gmx-users] Removal of global rotation/translation
jalemkul at vt.edu
Thu Jan 31 23:01:22 CET 2013
On 1/31/13 11:53 AM, George Patargias wrote:
> Dear Gromacs list
> I would like to ask a question regarding the global rotation and
> translation removal in GROMACS.
> In my mdp file I use the following options:
> ; mode for center of mass motion removal
> comm-mode = Linear
> ; number of steps for center of mass motion removal
> nstcomm = 10
> ; group(s) for center of mass motion removal
> comm-grps =
> Are these options ensuring that global rotation and translation is removed
> every 10 steps?
More directly, it removes net motion of the center of mass, thus avoiding
problems like the flying ice cube.
> Is the trjconv command (as issued below) also removing global rotation and
> trjconv -f traj_Total.xtc -s prod1.tpr -o rot+trans.xtc -fit rot+trans
Not necessarily global motions, but you can apply the fitting to whatever subset
of atoms you like.
> In which case is the "-center" option in trjconv is used?
Many. trjconv is sort of a Swiss army knife, capable of doing dozens of things
if the right options are applied. The -center option is probably most often
used to center a simple solute in the box in every frame.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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