On 8/29/13 5:15 PM, Gianluca Interlandi wrote:
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.
I would be very interested in reading about some of these reports. I have
searched the gromacs forum and I have found similar discussions but never
accompanied by actual benchmarks with numbers, or maybe I have not searched
carefully enough!
They tend to show up in reports of crashes, structures falling apart, and
failure to reproduce membrane properties (which is extremely sensitive to cutoff
values).
One such example that I recall having occurred recently:
http://lists.gromacs.org/pipermail/gmx-users/2013-January/078269.html
Previous posts in that thread have lots of information.
-Justin
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Justin A. Lemkul, Ph.D.
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