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

From: David A Case <>
Date: Tue, 22 Oct 2019 08:16:30 -0400

On Tue, Oct 22, 2019, Schröder, David Christopher wrote:
>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.

>Can I safely proceed with the -AllowSmallBox flag or does this need to be

My experience with -AllowSmallBox has been that problems still seem to
occur, so I don't think it is "safe". What cutoff and skinnb values are
you using? Setting them to 8.0 and 1.0 or 2.0 may allow the simulation
to continue (I don't know exactly what the calculation is for a
truncated octahedron.)

If that doesn't work, your two options are to make a bigger solvent box
(i.e. more DMSO molecules) or use the CPU version of the code. You
probably don't need a much bigger box, but you may have to experiment a
bit to find out what will work.

Amber's GPU code optimizations are agressive, and have never allowed for
small periodic unit cells. We really only have one developer (Dave
Cerutti) who groks this part of the CPU code, and the coding effort required to
accommodate small box sizes has been deemed too great, given the
relatively small demand for small systems and the potential workarounds
listed above.


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Received on Tue Oct 22 2019 - 05:30:02 PDT
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