Re: CUDA vd non-CUDA for minimization

From: Kenno Vanommeslaeghe (
Date: Fri Oct 18 2013 - 13:55:00 CDT

This has been discussed in great detail by Axel Kohlmeyer in a thread
titled "Equilibration of the membrane bilayers with CUDA-support" only 5
weeks ago. Search the archives (preferably before posting).

To summarize: the CUDA code is expected to run into trouble when given
strained structures that won't occur in a normal MD simulation.

On 10/18/2013 01:13 PM, Francesco Pietra wrote:
> Hello:
> With GTX-680 cards and cuda namd 2.9 I had problems for minimization,
> problems that I already encountered with other systems and previous
> versions of cuda namd.
> I refer to a difficult situation, where i had rotated a histidine residue
> in the protein and imposed rmsd colvars. With cuda namd only
> velocityQuenching could be run, while "minimization" resulted in atoms
> moving too fast (just in the area that I had modified) under a variety of
> settings.
> Turning to non cuda namd 2.9 "minimization" went on without problems. It
> seems that when the calculation of energy is most relevant, as during a
> minimization, CPUs are still a better choice.
> If true, I wonder whether free energy calculations with cuda are still to
> be taken with much reservation.
> thanks
> francesco pietra

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:47 CST