[gmx-users] free energy: annihilation

David Mobley dmobley at gmail.com
Tue Aug 29 19:56:14 CEST 2006


> It still seems strange, if one can get a lot of other properties
> correct, like DHvap, dielectric constant, density, diffusion constant etc.
> Unfortunately my simulations are converging very slowly, but I hope to
> have more conclusive results soon.

Ah, you checked all those things? I suspect in my case I would get
incorrect DHvap, etc depending on my charge set.

Yes, I would expect these to be pretty slow to converge: You're
dealing with a pretty big molecule. I run 5 ns for relatively small
molecules that don't even have any rotatable bonds.

> Reasonable Estimate of Simple Point charges...
> It's not that I know of any better method to do it, but the QM levels of
> theory typically used for computing charges are *very* low, and far from
> convergence to the basis-set limit. In addition RESP is not a good
> method, because the problem is underdetermined... You know, Peter
> Kollman once told me that they did quantum calculations followed by RESP
> and then multiplied the charges by 0.9.

So we have a preprint on this. We've done about 8 different levels of
QM going up to MP2/cc-PVTZ and B3LYP/cc-PVTZ, with and without
reaction field treatment of solvent.

I agree that RESP is not ideal, but I haven't seen anything that works
better. If you have, I'd love to hear about it. We're not, however,
doing anything strange like  multiplying by 0.9.

> <cynical>
> Or: for interesting molecules you're out of luck, unless you're lucky
> </cynical>

Exactly. :)

Or, in other words, we should worry about this far more than we do.


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