[gmx-users] Extracting enthalpies during or after MD

[Mark Abraham]

----- 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

> 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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