Re: [AMBER] Which shake option to be used

From: case <>
Date: Sun, 28 Mar 2010 09:35:24 -0400

On Sun, Mar 28, 2010, nicholus bhattacharjee wrote:

> I am using amber 9. In the tutorials provided with
> that for using SHAKE algorithm only ntc=2 is used and not ntc=3. I am not
> sure which is the standard protocol. Dose using different values of ntc=2 or
> 3 will considerably influence my results? Thank you in advance for the help.

The main reason is that jobs with ntc=3 cannot be run in parallel. Further,
for most situations, shakeing just the hydrogens (ntc=2) gives most of the
advantages of shaking all bonds, in terms to allow one to use a slightly
longer time step for integration.


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Received on Sun Mar 28 2010 - 07:00:02 PDT
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