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? > >> 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? 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? 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? > >> 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
