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