time per step during GPU-accelerated Implicit Solvent calculations

From: Thomas Albers (talbers_at_binghamton.edu)
Date: Sun Nov 15 2015 - 19:11:26 CST


I am looking at a 200-residue protein using implicit solvent. With 4
cores (Xeon E5504) and GPU acceleration (GTX 660), time per step is
initially 0.01 s, but after a few 100000 steps climbs to 0.025 steps
and more. No other program is taking up CPU cycles, and there's no
screensaver or anything that might tax the graphics card. What would
cause this strange behaviour, and what should be done?


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