Thank you both, I am close to solve it. The remaining problem is when I mdrun -rerun, it tells the number of atoms in old trajectory is not the same as chosen index file.
>Number of atoms in trajectory (24000) does not match the run input file (16) can you help me? Best regards On Fri, Jul 1, 2016 at 2:19 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > 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. > -- 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.