AMBER Archive (2004)

Subject: Re: AMBER: A question about pheTI in AMBER8 test.

From: David A. Case (
Date: Wed Aug 04 2004 - 18:38:52 CDT

On Wed, Aug 04, 2004, Chunhu Tan wrote:
> We find something strange on the pheTI in AMBER8 test files. Both the
> Run.0 and Run.p0 were passed, and as the Notes said, the results for Run.0
> mathched Run.p0. But when we turn on the SHAKE in these two input files,[
> add ntf=2 (or 3),ntc = 2 (or 3) in the mdin of Run.0 and Run.p0 ] , the
> results were very different. Is it a bug or something else?

This is expected. Shake cannot be applied to atoms that are being perturbed
(since the equilibrium bond lengths in the perturbed and unpertubed states
might be different). Hence, in the "standard" run Shake is being applied,
but not in the run using the perturbation prmtop file. So the results should
indeed differ.

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