Re: Alchemical calculations in CUDA version of NAMD?

From: Lela Vukovic (
Date: Wed Mar 03 2010 - 12:01:03 CST

Hello again,
the difference turned out to be in the PME settings. With same PME
settings, the calculation speeds of TI calculations and regular
dynamics in NPT ensemble are similar in CUDA built NAMD.

2010/3/3 Lela Vukovic <>:
> 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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