Dear Dr. Case:
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?
Thanks!
Chunhu
----- Original Message -----
From: "David A. Case" <case.scripps.edu>
To: <amber.scripps.edu>
Sent: Wednesday, August 04, 2004 4:38 PM
Subject: Re: AMBER: A question about pheTI in AMBER8 test.
> 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.
>
> ...dac
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Received on Fri Aug 06 2004 - 00:53:00 PDT
