On 8/28/13 7:28 PM, Gianluca Interlandi wrote:
Thanks for your replies, Mark. What do you think about the current DispCorr
option in gromacs? Is it worth it trying it? Also, I wonder whether using
DispCorr for LJ + PME for Cb justifies reducing the cutoff for non-bonded to 1
nm with the CHARMM force field, where 1.2 nm is usually recommended.
This is risky. Current CHARMM development relies on a 1.2-nm cutoff for LJ, so
that's how we balance all of the forces during parameterization. To me, ad hoc
changes like these are not worth the tiny (potential) increase in performance.
As I recently told someone else on this topic, if you're intent on fiddling with
the typical workings of a force field, especially if you're making changes to
something so fundamental, be prepared to undertake a demonstration that you can
recapitulate all of the expected outcomes of the force field or improve upon
them. My gut feeling, in this case and others, is that you won't be able to.
You're messing with something that is fairly critical to obtaining sensible results.
As for dispersion correction, it is generally helpful, but it assumes a
homogeneous environment. If you simulate with a membrane, for instance, this
assumption breaks down, though some literature suggests that use of dispersion
correction in these cases is still better than nothing.
-Justin
--
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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