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. 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? And does mdrun -rerun work on a parallel cluster? Best regards, Jesper > ----- 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
