[gmx-users] Extracting enthalpies during or after MD
mark.abraham at anu.edu.au
Fri Jun 4 01:24:15 CEST 2010
----- Original Message -----
From: lists at jsx.dk
Date: Friday, June 4, 2010 8:47
Subject: [gmx-users] Extracting enthalpies during or after MD
To: gmx-users at gromacs.org
> 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
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 .
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