[gmx-users] Long range Lennard Jones

[Justin Lemkul]

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
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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