AMBER Archive (2007)

Subject: Re: AMBER: large RMS fluctuations in turning off VDW interactions by TI

From: David Mobley (dmobley_at_gmail.com)
Date: Tue Jul 03 2007 - 14:55:54 CDT

David and all,

> I feel I should point out that Table 1 and Fig. 2 of the paper mentioned above
> show that you should be able to get good results, with low statistical
> uncertainties, using the klambda option of Amber8 or 9. The advantages of the
> soft-core potentials (at least in this study) are visible, but relatively
> minor. Thomas is travelling right now, but maybe when he reads this, he can
> post the RMS fluctuations from this studies.

As we discussed before, my previous testing had indicated the noise
was worse in the context of binding sites than for solvation free
energies (which are what were tested here). But I think Thomas is
going to look into this more.

David
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