[gmx-users] Long range Lennard Jones
jalemkul at vt.edu
Thu Aug 29 03:18:38 CEST 2013
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
PME is generally vastly better than switched or shifted electrostatics. This
has been demonstrated in the literature consistently over many years.
>> 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 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
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> gmx-users mailing list gmx-users at gromacs.org
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> Gianluca Interlandi, PhD gianluca at u.washington.edu
> +1 (206) 685 4435
> Research Scientist at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
Justin A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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