From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
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:
> 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
> 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.
> francesco pietra
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