On Wed, Nov 02, 2011, peker milas wrote:
>
> I would like to ask whether there is a way of calculating free energies for
> MD frames or not as a post-processing method. I read about MMPBSA.py but my
> problem is not as complicated as described in documentation of MMPBSA. I
> just want to calculate free energies of user specified residue(s) for each
> MD frame. So, is this possible ?
No. Free energy is an aggregate quantity the characterizes a thermodynamic
state (or a collection of MD snapshots that is supposed to represent that
state). It is not appropriate to think about the free energy of an individual
snapshot. And, although it is possible to approximately decompose free
energies on a residue-by-residue basis, such analysis always involves
heuristic approximations.
You might want to think about what you would do with the data you are asking
about. Maybe some other quantity (which could be calculated) would serve your
needs.
....dac
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Received on Wed Nov 02 2011 - 10:30:05 PDT
