[gmx-users] Re: Dumping of energies

David van der Spoel spoel at xray.bmc.uu.se
Tue Mar 4 19:50:36 CET 2008

andersle at stud.ntnu.no wrote:
>>> Dear all,
>>> I wonder if there is some way in gromacs to dump the potential energy
>>> (or internal energy) of each particle to the disk during a simulation.
>> No, because it isn't calculated.
>>> That is, something similar to the dumping of the positions, velocities
>>> and forces of the individual particles.
>>> Is there a way to do this out of the box in gromacs?
>>> Or has anyone done this by modifying the source?
>> Well, first you have to decide how to partition the energy arising from
>> each type of bonded interaction onto the participating atoms.
>> Actually, before that, I'd ask myself what I was hoping this
>> per-particle energy was going to tell me.
>> Mark
> For instance:
> - thermal conductivity (Green-Kubo relation)
> - energy fluctuations in different parts of a inhomogeneous system (e.g. 
> protein in water)

But the first question about HOW to partitition intramolecular energy 
remains. Even for intermolecular energy this is not straightforward, 
although the easiest way there is to divide evenly  between molecules.

> Anders
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David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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