[gmx-users] Removal of global rotation/translation

[Justin Lemkul]

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
> translation?
>
> 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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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