Dear amber users & developers,
after I reinstalled amber16 yesterday with all patches applied I observe following
error message when starting a new MD production run. I also tested rerunning a previous
calculation.
The system is a small 5 residue cyclic peptide in DMSO solvent box.
The trunc octah. box has a size of 35.8 and contains 3043 Atoms.
gpu_neighbor_list_setup :: Small box detected, with <= 2 cells in one or more
dimensions. The current GPU code has been
deemed unsafe for these situations. Please alter the
cutoff to increase the number of hash cells, make
use of the CPU code, or (if absolutely necessary)
run pmemd.cuda with the -AllowSmallBox flag. This
behavior will be corrected in a forthcoming patch
of Amber 18.
Can I safely proceed with the -AllowSmallBox flag or does this need to be patched?
Thanks for your help,
David Schroeder
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Received on Tue Oct 22 2019 - 02:00:02 PDT
