[gmx-users] Removal of global rotation/translation

[George Patargias]

Many thanks for this Justin.
>
>
> 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
>
> --
> ========================================
>
> 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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Dr. George Patargias
Postdoctoral Researcher
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27
Athens
Greece

Office: +302106597568