----- 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
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