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.
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.
Gianluca
-----------------------------------------------------
Gianluca Interlandi, PhD gianl...@u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
http://healthynaturalbaby.org
-----------------------------------------------------
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