Re: accelMDdihe is not working properly in NAMD after commit e3e849639982dcba9a60c6072c81fdb7cba69759

From: David Hardy (
Date: Thu May 17 2018 - 10:46:00 CDT

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,
> On May 15, 2018, at 8:59 PM, yjcoshc <> 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.
> Thanks,
> Haochuan Chen

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