Many thanks Mark. I am sorry I need more help:
If you're selecting different molecules for different frames, then simple > mdrun -rerun can't cope, because the energy groups are constant over the > rerun. Probably you want something like > > make a tpr that will evaluate the energy for each pair (e.g. with tpbconv > and a static selection in an index group) I see only one group can be selected here. right? then how the mdrun -rerun produces energy between different groups? > for each frame of the trajectory > make dynamic selection > use selection to get molecule subset of frame via trjconv > use mdrun -rerun with the above tpr and the subset of the frame > Should I change the energy group names in in original .mpd file according to the above first step before this mdrun? > > Mark > > On Wed, Jul 13, 2016 at 9:59 AM Faezeh Pousaneh <fpoosa...@gmail.com> > wrote: > > > Dear Justin, > > > > I have a question regarding my last question (below which was 'obtaining > > energy for different selections'). > > > > My selection is a molecule within specific z of the box. I want the > > selected z remains fix for whole energy calculation. I realized that > mdrun > > -rerun does not update the position of the selection for all frames. > > Therefore, I guess one needs first to make a 'dynamic' selection from > > g_select. The resulted index file then contains selections for all > frames > > written frame by frame. Now, I suppose one can go for mdrun -rerun with > the > > given index file. However, my question now is how properly re-name the > > energy groups in .mdp file according to the index file which has so many > > frames? > > > > Thank you for help. > > > > Best regards > > > > > > On Fri, Jul 1, 2016 at 4:20 PM, Faezeh Pousaneh <fpoosa...@gmail.com> > > wrote: > > > > > Thank you again :) > > > > > > > > > Best regards > > > > > > > > > On Fri, Jul 1, 2016 at 4:17 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > >> > > >> > > >> On 7/1/16 10:05 AM, Faezeh Pousaneh wrote: > > >> > > >>> 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: > > >>> > > >>> > > >> For the sake of correctness in the archive, don't do this: > > >> > > >> tc-grps = resnr_5_to_6000 resnr_1_to_4 > > >>> > > >> > > >> For the purpose of a re-run, tc-grps being split this way has no > effect. > > >> But one should absolutely not divide thermostatting groups in this > way. > > >> > > >> I feel it is important to point out so that (1) people don't make > this a > > >> common practice and (2) you don't start re-using .mdp files with these > > >> settings. > > >> > > >> This is all you need to accomplish what you want in terms of the > energy: > > >> > > >> energygrps = resnr_5_to_6000 resnr_1_to_4 > > >>> > > >>> > > >> The rest of the .mdp file should be the same as your original run. > > >> > > >> -Justin > > >> > > >> > > >> 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. > > >>>> > > >>>> > > >> -- > > >> ================================================== > > >> > > >> 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. > -- 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.