Re: [AMBER] How to use a relatively smaller cutoff in the GB simulation

From: David A Case <>
Date: Wed, 23 Jun 2021 08:48:49 -0400

On Wed, Jun 23, 2021, jinfeng liu wrote:
>I am simulating a huge protein system by using the GB model. I know that
>the GB simulation requires cut > 999.

This is true for pmemd.cuda, and there is no alternative (that I know of.)
For CPU executables, you can use smaller values.

You might also want to consider the GB-HCP model, which is designed for very
large systems. See section 42.5 in the Amber 2021 Reference Manual.
There's a learning curve to get this going, but it might do what you want,
depending on what you mean by the word "huge", above.


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Received on Wed Jun 23 2021 - 06:00:03 PDT
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