From: Lela Vukovic (lvukov1_at_gmail.com)
Date: Wed Mar 03 2010 - 11:33:36 CST
In the NAMD tutorial, it says that alchemical free energy perturbation
calculations are not available in CUDA built NAMD.
However, thermodynamic integration calculations do run in CUDA-built
NAMD, and, in my experience, they are not accelerated as the
calculations performed for regular NPT dynamics of the same system.
Since energy evaluation is done on CPUs, and in these calculations,
the output is the derivative of energy, I tried decreasing the
frequency of output for this derivative. But, the calculation speed
does not seem to be affected by this.
So, my question is if CUDA-built NAMD is going to have alchemical
calculations available to run at accelerated rates? If not, is there
an intrinsic limitation to accelerating this type of calculations by
use of GPUs (as only nonbonded force evaluation is performed on GPUs)?
Department of Chemistry
University of Illinois at Chicago
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Chicago, IL 60607
Tel. (312) 996-1531
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