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 > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > * 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
Dr. George Patargias Postdoctoral Researcher Biomedical Research Foundation Academy of Athens 4, Soranou Ephessiou 115 27 Athens Greece Office: +302106597568 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
