On Mon, May 30, 2011, Bernhard Poll wrote:
>
> I read the description but this wasn't totally clear to me to be honest. So
> just to be save: Re-run the simulation with default dielectric constant and
> then changing it during mmpbsa/gbsa calculation?
There is really only one way to carry out an explicit solvent simulation,
since all dielectric behavior is being explicitly modeled. So, if you didn't
save the trajectory with the default dielc, you will have to re-run it.
It is possible to change the parameters of the continuum solvent model that is
used to analyze the resulting energetics: you could use the same trajectory
for several mmpbsa runs, choosing different dielectric models.
As an aside, not that I do *not* recommend doing any of this: the MD
simulation itself averages over fluctuations in the solute coordinates, which
is what is also described by using a dielectric constant other than 1 in
continuum solvent models. Hence, there is a real danger of double-counting.
I understand that papers are published that explore what happens, but am not
personally convinced that any systematic gain in insight is obtained by
allowing the internal dielectric constant to become a parameter. Opinions, of
course, may vary here, and I don't want to discourage exploration.
...hope this helps....dac
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Received on Mon May 30 2011 - 08:30:02 PDT
