Hi, Yes as Justin says, a group is a few molecules that you selected :-)
Mark On Fri, 1 Jul 2016 14:00 Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/1/16 7:55 AM, Faezeh Pousaneh wrote: > > Thank you Mark, I see. But what is the solution then? The way you > proposed > > > > ''You can make a new .tpr file with those > > energy groups and use mdrun -rerun on the old trajectory, however.'' > > > > is not my answer, since I do not want the energy for a ''group'' of > > molecules, rather for specified combination of few molecules I define > from > > g_select. > > > > The only function available is to define energygrps in the .mdp file, > supply an > index file with those groups (e.g. from g_select) and do as Mark says and > re-calculate those interaction energies with mdrun -rerun on the existing > trajectory. The short-range nonbonded interaction energies between those > groups > will be written to their own terms in a new .edr file. > > -Justin > > > > > Best regards > > > > > > On Fri, Jul 1, 2016 at 11:20 AM, Mark Abraham <mark.j.abra...@gmail.com> > > wrote: > > > >> Hi, > >> > >> The .edr file contains only what was written during the simulation, and > >> that was for any energy groups defined before that run. You're trying to > >> ask it to make an arbitrary repartition, which it can't do unless it > >> recorded every component of the energy for every frame (which would take > >> forever and use lots of disk). You can make a new .tpr file with those > >> energy groups and use mdrun -rerun on the old trajectory, however. > >> > >> Mark > >> > >> On Fri, Jul 1, 2016 at 9:41 AM Faezeh Pousaneh <fpoosa...@gmail.com> > >> wrote: > >> > >>> Hi > >>> > >>> Does someone know how to obtain energy between specific molecules in > the > >>> system? > >>> > >>> What I did and seems not be correct is: > >>> 1- I obtained the molecules I wanted to look at: > >>> g_select_mpi -f 600gro.gro -s production.tpr -on > >>> > >>> 2- Then I produced a .tpr file for the chosen selection,index.ndx, > >>> tpbconv -s production.tpr -n index.ndx -o tpxout.tpr > >>> > >>> 3- Finally put the created .tpr file as an input for g_energy > >>> g_energy -f ener.edr -s tpxout.tpr (either, g_energy -s tpxout.tpr) > >>> > >>> But that is not the solution, since it gives energy for whole system. > >>> Best regards > >>> -- > >>> 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. > >> > > -- > ================================================== > > 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.