Hi Amber community
I am trying to simulate a cyclic peptide of 8 residues and am using a TIP3P
waterbox. I had kept a box size of 9 Angstrom while running LEaP. On
trying to run the production run, this is the error that I am getting:
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.
Can you please help me solve this?
The equilibrated structure looks fine within the water box and shows enough
space on each side. Yet, why do I get this error?
Thanks
Suchetana Gupta
University of Oregon
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Received on Mon Mar 21 2022 - 17:00:03 PDT
