CUDA vd non-CUDA for minimization

From: Francesco Pietra (
Date: Fri Oct 18 2013 - 12:13:04 CDT

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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