Re: Alchemical calculations in CUDA version of NAMD?

From: Chris Harrison (
Date: Wed Mar 17 2010 - 02:37:21 CDT


Alchemical methods (FEP, TI, & related methods like LES) do not currently
utilize GPU-accelerated calculations.

Alchemical calculations will make it onto the GPU, but not within the next
few months.

If you still require an answer to your last question, please clarify it.


Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                            Voice: 217-244-1733               Fax: 217-244-6078
On Wed, Mar 3, 2010 at 12:33 PM, Lela Vukovic <> wrote:
> 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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