Re: metadynamics

From: Axel Kohlmeyer (
Date: Fri Apr 26 2013 - 09:53:41 CDT

On Fri, Apr 26, 2013 at 4:46 PM, Francesco Pietra <> wrote:
> Hello:
> This is to ask whether there is any plan to extend NAMD-CUDA to
> bias-exchange metadynamics, temperature-exchange metadynamics, and
> reconnaissance metadynamics. This is just to plan with my work.
> I was not careful enough to appreaciate that PLUMED-NAMD is at a single
> processor. I compiled NAMD2.9-CUDA4.0 with PLUMED1.3, including recon, and
> it seemed to run on multiple GPUs, by inserting commands for PLUMED into the
> NAMD conf file (just a "distance" job on a large protein I was engaged
> with). According to nvidia-smi, all GPUs were involved, and the log file
> showed PLUMED involved. Now, having been informed that PLUMED is at a single
> CPU with NAMD, it must have been fake success.

it is not fake, it just shows that you know little about parallel
programming, GPU acceleration, and code optimization.


> Thanks
> francesco pietra

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.

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