From: Alexander Adams (xadams_at_umich.edu)
Date: Tue Aug 07 2018 - 11:43:30 CDT
Dear NAMD developers,
I was wondering if this aMD dihedral boost issue has been fixed or if we
should still use the bondedCUDA workaround.
Thanks in advance for your time,
University of Michigan, Ann Arbor
Ph.D. Candidate - Mayes, Glotzer Labs
College of Engineering - Chemical Engineering
On Thu, May 17, 2018 at 11:46 AM, David Hardy <dhardy_at_ks.uiuc.edu> wrote:
> Dear Haochuan,
> Thanks for bringing this to our attention.
> Until we can get the CUDA kernel for dihedrals working correctly for
> accelerated MD, it is possible to disable just the dihedral part of the
> calculation. bondedCUDA is actually treated as a bit field that can enable
> (or disable) the individual term types:
> 1 = bonds
> 2 = angles
> 4 = dihedrals
> 8 = impropers
> 16 = exclusions
> 32 = crossterms
> You should be able to do your calculation correctly by setting bondedCUDA
> = 251 (i.e. 255-4) to disable just the dihedral calculation on the GPU but
> use the GPU for everything else.
> Apologies for the half-baked interface, which was never really intended to
> be exposed for normal NAMD use.
> Best regards,
> David J. Hardy, Ph.D.
> Beckman Institute
> University of Illinois at Urbana-Champaign
> 405 N. Mathews Ave., Urbana, IL 61801
> dhardy_at_ks.uiuc.edu, http://www.ks.uiuc.edu/~dhardy/
> On May 15, 2018, at 8:59 PM, yjcoshc <yjcoshc_at_gmail.com> wrote:
> Dear NAMD developers,
> Recently I have found the dihedral boost potential of accelerated MD (amd)
> doesn't affect the real distribution of dihedral angles. After some
> debugging the issue disappears if I add "bondedCUDA 0" to the NAMD
> configuration file. I have a look at the git commit
> e3e849639982dcba9a60c6072c81fdb7cba69759, which offloads the bonded terms
> to GPU but misses computing the aMD dihedral force.
> Haochuan Chen
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