Current CHARMM development relies on a 1.2-nm cutoff for LJ, so that's
how we balance all of the forces during parameterization.
Ok, I agree. What about the use of PME for Coulomb? The CHARMM PARAM22
force field was parametrized using SHIFT on electrostatic forces making it
zero after 12 A (please note that SHIFT and FSHIFT in CHARMM greatly
differ from the gromacs-style Shift). Also, the CHARMM switch function is
different from gromacs Switch (at least from what I can tell reading pages
71-72 of the gromacs manual 4.6.3).
Thanks,
Gianluca
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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