**From:** Lela Vukovic (*lvukov1_at_gmail.com*)

**Date:** Wed Mar 03 2010 - 11:33:36 CST

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Hello,

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)?

Thank you,

Lela Vukovic

~~~~~~~~~~~~~~~~~~~~~~~~~~

PhD candidate

Department of Chemistry

University of Illinois at Chicago

845 W Taylor St., Room 4500

Chicago, IL 60607

Tel. (312) 996-1531

~~~~~~~~~~~~~~~~~~~~~~~~~~

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