Aaah, I get it now (finally)... Thanks again... Jesper
> > > ----- Original Message ----- > From: li...@jsx.dk > Date: Saturday, June 5, 2010 5:58 > Subject: Re: [gmx-users] Extracting enthalpies during or after MD > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > >> Thanks for the help Mark. Just to make sure I understand you >> correctly, I >> have a few comments/questions, see below... >> >> kind regards, >> Jesper >> >> > ----- Original Message ----- >> > From: li...@jsx.dk >> > Date: Friday, June 4, 2010 10:35 >> > Subject: Re: [gmx-users] Extracting enthalpies during or after MD >> > To: Discussion list for GROMACS users <gmx-users@gromacs.org> >> > >> >> Hi Mark, >> >> >> >> Thanks for the quick reply. >> >> >> >> The thing with the energy groups makes sense now. But I have >> run into >> >> another problem with the method... >> >> >> >> The same atom cannot be in multiple energy groups during a >> simulation.> >> > It doesn't want to be... see manual 3.3 >> >> And there is no way to force it to be, right? > > Correct. The nonbonded loops tend to be (roughly) loops over energy groups > over charge groups. > >> >> Let say that I want the interaction energy between water and lipid >> >> head-group and also water and protein. Will I then have to do >> "mdrun>> -rerun" to get all the energy group I want out of this? >> > >> > One (re)run will suffice unless you have large numbers of >> groups. Consider >> > whether g_enemat is useful for you. >> >> >> Using rerun will I be able to specify more energy groups, where >> the same >> atom can be in multiple groups? Else, I would have to run it several >> times, right? > > No. Read manual 3.3 carefully - "mutual interactions between all energy > monitor groups are compiled during the simulations". So you can get > protein-lipid-head-group and protein-solvent (and the other pairs, > including self-self, unless you use energy group exclusions) merely by > defining three non-intersecting energy groups. > >> Also, g_enemat is to post-process/analyse the numbers once I >> have them >> from a simulation, where I have extracted all the energy numbers >> I want, >> right? > > Yes. g_enemat -h. > >> So if I cannot do it with one simulations (because some atoms >> are part of >> several different energy groups, then g_enemat won't work for my case, >> correct? > > You can do it with one invocation of mdrun, which is why I suggested that > :-) > > Mark > >> >> And does mdrun -rerun work on a parallel cluster? >> > >> > Yes, it's exactly like mdrun, but derives the next positions >> from the >> > trajectory, not from integration. If your groups are small, >> then use of >> > energy group exclusions will make the problem small enough >> that you don't >> > need parallelism, however. >> > >> > Obviously these interaction energies won't mean anything if >> you're using >> > PME, since the long-range term can't be decomposed. >> > >> > Mark >> > >> >> > ----- Original Message ----- >> >> > From: li...@jsx.dk >> >> > Date: Friday, June 4, 2010 8:47 >> >> > Subject: [gmx-users] Extracting enthalpies during or after MD >> >> > To: gmx-users@gromacs.org >> >> > >> >> >> Hello, >> >> >> >> >> >> I am wondering if it is possible to output interaction >> >> >> energies/enthalpiesduring an MD simulation between specific >> >> >> groups of atoms. >> >> > >> >> > Yes. Look up "energy groups" in the manual. >> >> > >> >> >> The energies are all calculated anyways before the forces are >> >> >> calculated,so I am wondering if there is an option to output >> >> >> those energies to a >> >> >> file? >> >> > >> >> > They'll go to the .edr file and be accessible with (e.g.) >> g_energy>> > >> >> >> I saw someone on the list who had re-coded gromacs to >> output these >> >> >> energies, but this resulted in a significant slowdown of the >> >> >> simulationbecause he made the code perform output in an >> inner-loop. >> >> > >> >> > Yep, don't do that. >> >> > >> >> >> If this is not an option, is there a clever way to get these >> >> >> numbers out >> >> >> after having run the simulation. Essentially, what I want >> is to >> >> >> get the >> >> >> enthalpy, between e.g. a PO4 head-group bead and a C1A >> tail-bead >> >> >> using the >> >> >> Martini FF. >> >> > >> >> > You can implement the above to happen during your simulation, >> >> or use the >> >> > facility of mdrun -rerun on a previously computed trajectory >> >> with a >> >> > suitable .tpr to recompute only the energies of the groups of >> >> interest . >> >> > >> >> > Mark >> >> > >> >> > -- >> >> > gmx-users mailing list gmx-users@gromacs.org >> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users >> >> > Please search the archive at http://www.gromacs.org/search >> >> before posting! >> >> > Please don't post (un)subscribe requests to the list. Use the >> >> > www interface or send it to gmx-users-requ...@gromacs.org. >> >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> >> -- >> >> gmx-users mailing list gmx-users@gromacs.org >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> >> Please search the archive at http://www.gromacs.org/search >> >> before posting! >> >> Please don't post (un)subscribe requests to the list. Use the >> >> www interface or send it to gmx-users-requ...@gromacs.org. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > -- >> > gmx-users mailing list gmx-users@gromacs.org >> > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > Please search the archive at http://www.gromacs.org/search >> before posting! >> > Please don't post (un)subscribe requests to the list. Use the >> > www interface or send it to gmx-users-requ...@gromacs.org. >> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search >> before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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