On 8/28/13 9:09 PM, Gianluca Interlandi wrote:
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).
PME is generally vastly better than switched or shifted electrostatics. This
has been demonstrated in the literature consistently over many years.
-Justin
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.
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Gianluca Interlandi, PhD gianl...@u.washington.edu
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Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
http://healthynaturalbaby.org
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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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