----- Original Message -----<br>From: lists@jsx.dk<br>Date: Friday, June 4, 2010 8:47<br>Subject: [gmx-users] Extracting enthalpies during or after MD<br>To: gmx-users@gromacs.org<br><br>> Hello,<br>> <br>> I am wondering if it is possible to output interaction <br>> energies/enthalpiesduring an MD simulation between specific <br>> groups of atoms.<br><br>Yes. Look up "energy groups" in the manual.<br> <br>> The energies are all calculated anyways before the forces are <br>> calculated,so I am wondering if there is an option to output <br>> those energies to a<br>> file?<br><br>They'll go to the .edr file and be accessible with (e.g.) g_energy<br><br>> I saw someone on the list who had re-coded gromacs to output these<br>> energies, but this resulted in a significant slowdown of the <br>> simulationbecause he made the code perform output in an inner-loop.<br><br>Yep, don't do that.<br><br>> If this is not an option, is there a clever way to get these <br>> numbers out<br>> after having run the simulation. Essentially, what I want is to <br>> get the<br>> enthalpy, between e.g. a PO4 head-group bead and a C1A tail-bead <br>> using the<br>> Martini FF.<br><br>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 .<br><br>Mark