Re: metadynamics

From: Francesco Pietra (
Date: Fri Apr 26 2013 - 10:58:40 CDT

Hi Niklaus:
That helps. Sorry for having misunderstood. I have reexamined the log and
everything is in order, like it was the output of nvidia-smi and "top -i"

On Fri, Apr 26, 2013 at 5:17 PM, Niklaus Johner <>wrote:

> Hi,
> My understanding is that PLUMED does indeed use only one processor, but
> this is just for the calculations needed for your collective variable,
> which is usually very small compared to the processing that has to be made
> for all the forces in the system. The latter are still spread on multiple
> processors and the GPUs. Therefore this doesn't slow down your namd run
> (except in some extreme cases, such as using as collective variable the
> contacts between two large sets of atoms for example).
> You should see that right away form the performance of your runs anyway,
> but I have used PLUMED-NAMD with GPUs and it works fine.
> N.
> Niklaus Johner
> Weill Cornell Medical College
> Harel Weinstein Lab
> Department of Physiology and Biophysics
> 1300 York Avenue, Room D-501
> New York, NY 10065
> On Apr 26, 2013, at 10:46 AM, 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.
> Thanks
> francesco pietra

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