You should follow the message and increase your cutoff. Otherwise, use a
larger buffer when you solvate the peptide in leap.
On Mon, Mar 21, 2022, 4:41 PM Suchetana Gupta <tutulg.gmail.com> wrote:
> 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 Tue Mar 22 2022 - 07:00:03 PDT
