On Sun, Dec 28, 2014, Abhilash J wrote:
>
> I have a MD trajectory wit water, protein and one other compound. I am
> interested in the enthalpy of the protein only over each frame the
> trajectory.
> I believe there must be some command in cpptraj or other AMBER modules
> which can be of help to me. I tried finding it but am still unable to
> locate it.
The entire system has an enthalpy, which is close to its average energy in
condensed phase, but this cannot be decomposed into a term for the "protein
only", either experimentally or computationally, since the energy terms are
not pairwise decomposable.
You could strip the solvent and compute the average energy of the (gas-phase)
protein. But this completely ignores the (very imporant) protein-solvent
contribution (and the interaction of the protein with the other compound.)
Furthermore, all molecular mechanics energies have an arbitrary zero, so only
energy differences have any meaning.
You should think carefully about exactly what you want to compute, and what
use you would make of the resulting number.
...good luck....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Dec 28 2014 - 06:30:02 PST
