Is there a limit for number of atoms that can be included in group(s) while using COM restraints with pmemd.cuda v18?
I am seeing significant divergence in restraint energy term between CPU and GPU version, for groups with about 50 atoms. For smaller groups with ~20 atoms, GPU simulations appear to be stable and comparable to CPU version. However, for groups with ~50 atoms the restraint energy term is showing "*********" within ~2000 steps (= 4 ps), while CPU simulations are stable for same input.
All patches have been applied including the relevant patch.7. Any pointers will be highly appreciated, and I am happy to provide more details.
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Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)
Web: http://www.agarwal-lab.org/
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Received on Sun Mar 10 2019 - 12:00:03 PDT
