[AMBER] error while running pmemd.cuda after reinstallation of amber 16

From: Schröder, David Christopher <dschroeder.uni-bielefeld.de>
Date: Tue, 22 Oct 2019 08:36:16 +0000

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
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
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