From: Jason Swails (jason.swails_at_gmail.com)
Date: Wed May 14 2014 - 10:20:57 CDT
On Wed, 2014-05-14 at 13:50 +0000, Michael Bellucci wrote:
> Thank you Jason. Your approach makes quite a bit more sense to me. I
> did see the pairInteraction keyword that NAMD has and I will look into
> using it further. As a quick hack, that is, without modifying the
> source code, I wonder if it would make sense or be possible to use the
> thermodynamic integration portion of the code to do the scaling. That
> is, would it make sense to turn on thermodynamic integration, flag the
> solute or solvent to be perturbed in the pdb, and then run MD with a
> particular value of lambda? Theoretically this should have the same
> effect, but as Axel suggested, accuracy may be a concern. It isn't a
> very satisfying solution, but it might suffice for a quick and dirty
> calculation.
My experience with NAMD has been very limited. I don't know if using
the TI code will work for what you are trying to do (does NAMD use a
dual topology approach? single topology? how are the end states
defined?). If you _can_ use it for your problem, then there should not
be any accuracy concerns *specifically with regards to how long-range
electrostatics are treated* -- they should be rigorously correct (unless
NAMD _does_ neglect long-range contributions to dV/dlambda -- but I find
this unlikely). Of course finite sampling and force field errors
introduce inaccuracies, but that's another topic.
HTH,
Jason
-- Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher
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