Re: [AMBER] Setting PME cutoff in Crystal Simulations

From: David A Case <david.case.rutgers.edu>
Date: Mon, 4 Jan 2021 08:14:34 -0500

On Sun, Jan 03, 2021, Matthew Guberman-Pfeffer wrote:
>
>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 ,

There is no direct fix to this problem, and it is unlikely (in spite of the
error message) that anything will change soon. You have a couple of
options:

1. You could try to slightly *decrease* the cutoff (say to 9 or even 8 ).
It is the ratio of the cell size to the cutoff that is important here.
The default cutoff is 8 , and that value is OK for many protein crystal
simulations.

[Aside: could you quote the exact error message, so that I could look for it
in the code? I don't think(?) it should be saying that the cutoff is too
small, but maybe I don't know exactly what error message you actually
triggered.]

2. If you are (understanably) leery about ignoring some Lennard-Jones
interactions beyond a smaller cutoff, you need to simulate a bigger system.
The usual procedure is to create a supercell consisting of several unit
cells. The advantage here is that you are now simulating N proteins
simultaneously, and so get better statistics and more sampling. The
physical realism is also greater: on average, the structure of the protein
is the same in each unit cell, but at any given point in time, each unit
cell will have its own conformation.

[Substitute the word "protein" above as appropriate.]

...good luck...dac


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Received on Mon Jan 04 2021 - 05:30:02 PST
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