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
non-negligible.
-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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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