AMBER Archive (2004)

Subject: Re: AMBER: ntt parameter

From: David A. Case (case_at_scripps.edu)
Date: Wed Dec 01 2004 - 18:14:30 CST

On Wed, Dec 01, 2004, tang kwa wrote:
>
> I would like to perform simulation which the distance
> is restrained. What is the difference between using
> NTT=1 and 3? Can I use NTT=3 in the explicit water
> system?

You should study the papers cited in the manual, under ntt=1, and gamma_ln.
It would not generally make good physical sense to use ntt=3 with explicit
water, but there might be situations where you would want to do that.
Neither option has much to do with distance restraints.

...dac

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