[gmx-users] Long range Lennard Jones

Justin Lemkul jalemkul at vt.edu
Thu Aug 29 22:57:32 CEST 2013

On 8/29/13 2:52 PM, Gianluca Interlandi wrote:
>> That's good to know that you've tested different setups.  Are the water
>> interaction energies comparable?  Have you tested model compounds or just full
>> proteins?  Over how long of a time period?
> I have tested only full proteins over a 50-ns period. I have not calculated yet
> the water interaction energies. Do you mean by that just the force field
> interaction energy bulk-bulk? I plan to test how much it affects FEP calculations.

I'm thinking more along the lines of the underlying CHARMM parameterization - MM 
water interaction energies between model compounds and whether or not the new 
cutoffs recapitulate the original CHARMM MM energies with the "standard" values.

>>> Finally, I have not tested it in gromacs, but in NAMD there is a performance
>>> gain of 25% when using the shorter cutoff. This is a factor to consider. When
>>> I asked for Teragrid supercomputing allocations back in 2006 and 2007 and I
>>> suggested 10/12/14 cutoff, the reviewers always complained and cut my
>>> requested time of 20% with the justification that I must use a shorter cutoff.
>> That's unfortunate.  In my opinion, it is shameful that desired performance
>> exceeds proven integrity of the data.
> I mean, performance is a factor to consider when accuracy is not affected. I
> don't recall what the reviewer's reasoning was. They probably did their
> recommendation in good faith that it won't affect accuracy. But I agree that one
> should test how much the system is affected.

Of course, if accuracy is not in question then performance dominates.  I have 
seen countless reports on this list and elsewhere where small changes in cutoffs 
lead to wildly incorrect behavior, affecting every force field.  Thus, I am 
always extremely skeptical of such changes.  The effects can be subtle but 



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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