Thank you Justin and Mark for the help. I could obtain. More details for someone with similar question:
1- First I defined the molecules (resnr 1 to 4) I wanted to look at (from existing simulation: production.tpr 6000wat.gro) : g_select -f 6000wat.gro -s production.tpr -on index.ndx resnr 1 to 4 resnr 5 to 6000 (all other renaming molecules also must be defined as next group, resnr 5 to 6000) 2- Then I looked at the name of groups created in the index file and changed the current .mdp file to include those groups: tc-grps = resnr_5_to_6000 resnr_1_to_4 energygrps = resnr_5_to_6000 resnr_1_to_4 3- Finally rerun grompp -f new.mdp -c 6000wat.gro -p topol.top -o new.tpr -n index.ndx mdrun -rerun traj.xtc -s new.tpr -mn index.ndx 4- So, if you now run g_energy you'll find those specified groups energies. Best regards On Fri, Jul 1, 2016 at 2:38 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 7/1/16 8:36 AM, Faezeh Pousaneh wrote: > >> 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) >> >> > Your .tpr file needs to contain the same system that you ran before. The > only thing that changes is the energygrps setting in the .mdp file. > > -Justin > > > 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. >>> >>> > -- > ================================================== > > 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? 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