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. 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. > -- 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.