[AMBER] Setting PME cutoff in Crystal Simulations

From: Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>
Date: Sun, 3 Jan 2021 15:37:09 -0500

Dear Amber Community,

I’m trying to apply the constant redox methodology to a metalloprotein in the crystalline state, and one question I have is: How do I determine the appropriate cutoff for PME?

From prior experience, I know that if I add 7200 waters, equilibrate with NPT, and add another 500 waters, I’m able to maintain the experimental volume if the crystal within 1%. However, when running the NPT equilibration on GPUs, I got an error message that the cutoff was too small, that using GPUs was unsafe, and that this issue would be corrected in a future release. I tried increasing the cutoff from 10 to 20 Å, but received a different error message, this time that the cutoff was larger than the sphere size (I’m not sure what it was referring to). If anyone is aware of the error messages I’m encountering—I regret not documenting them verbatim—or would like to share general advice about how to set the PME cutoff for crystal lattice simulations, I’d greatly appreciate the assistance.

Best regards,
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Received on Sun Jan 03 2021 - 13:00:02 PST
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