[gmx-users] Extracting enthalpies during or after MD

lists at jsx.dk lists at jsx.dk
Fri Jun 4 02:34:19 CEST 2010

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,

> ----- 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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