[gmx-users] Removal of global rotation/translation
gpat at bioacademy.gr
Sat Feb 2 21:21:46 CET 2013
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
>> 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
>> 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
> 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
> if the right options are applied. The -center option is probably most
> used to center a simple solute in the box in every frame.
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Dr. George Patargias
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
More information about the gromacs.org_gmx-users