----- 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
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