AMBER Archive (2004)

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

From: David A. Case (case_at_scripps.edu)
Date: Thu Aug 05 2004 - 19:39:06 CDT

On Thu, Aug 05, 2004, Chunhu Tan wrote:
>
> Thank you for your answer, but I am still confused about it. The
> question is , if we should always turn off shake when we use the
> perturbation prmtop file? If so, how about the water? If I turn on shake
> when the solute molecule is perturbed, maybe the shake act only on the
> water moleculs and have no effect on the solute, am I right?

Yes: this is correct. The perturbation code turns of shake for any atoms
that are being pertubed. SHAKE on non-perturbed atoms would still be there
if SHAKE is turned on with the ntc variable.

Unfortunately, this restriction makes it very difficult to perturb water
molecules, which need to be rigid in most simple models, like TIP3 or TIP4.
We will try to put together a fix for this limitation.

...dac

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