[gmx-users] Long range Lennard Jones

Gianluca Interlandi gianluca at u.washington.edu
Thu Aug 29 03:09:26 CEST 2013

> 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).



> 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
> -- 
> ==================================================
> 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
> ==================================================
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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.

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