To whom may have similar problem, that is how I solved it: First of all, Gromacs by default uses center of mass removal (at least in versions I use), but that is for 'whole system'. In my case I have a two-component system and I am interested in collecting density for one of the components. So, I used -fit obtain in trjconv to remove transnational movement of component 2:
trjconv_mpi -fit translation -s production.tpr -f traj.xtc -o OUTPUT.xtc chose component 2 and 2, Then, I collect densities from produced OUTPUT.xtc. Best regards On Fri, Nov 13, 2015 at 1:38 PM, Faezeh Pousaneh <fpoosa...@gmail.com> wrote: > Justin, thanks for comment. > In fact I am going to analyze g_density, but I see center of mass moves. I > have two-component system which has phase separated after a very long time. > I can't redo the simulation. > I could not mange that by tajconv. > Can I take the final .gro file of current simulation and run it with COM > removal to collect density? > > > Best regards > > > On Fri, Nov 13, 2015 at 1:30 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 11/13/15 4:06 AM, Faezeh Pousaneh wrote: >> >>> Hi, >>> >>> Please some one help me how to remove center of mass motion in a >>> trajectory >>> which is already created without this setting? is that possible? >>> >>> >> Not using COM motion removal during the run leads to artifacts; no amount >> of post-processing will fix that. If you're just looking to re-center some >> molecule(s) of interest, that's what trjconv is for. >> >> -Justin >> >> -- >> ================================================== >> >> Justin A. Lemkul, Ph.D. >> Ruth L. Kirschstein NRSA Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 629 >> University of Maryland, Baltimore >> 20 Penn St. >> Baltimore, MD 21201 >> >> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >> http://mackerell.umaryland.edu/~jalemkul >> >> ================================================== >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.