AMBER Archive (2006)

Subject: Re: AMBER: NTT for production run

From: David A. Case (
Date: Tue Mar 14 2006 - 19:49:46 CST

On Tue, Mar 14, 2006, Vlad Cojocaru wrote:
> ntt=1 with a higher tautp (weak coupling) should be preferred ...

ntt=1 has a the least effect on *dynamics*, and probably works pretty
well with a large tautp (>2.0). However, if you are really interested
in dynamics, you should set ntt=0 for production; one a system is
equilibrated, there is often no need for further temperature regulation.

ntt=3 will most reliable get you a canonical distribution of configurations.
You should prefer this for free-energy simulations, for example.

There are many bad things that can happen with ntt=1, especially with small
values of tautp. The Amber 9 Users' Manual has the following sentence
(in italics): "Please don't use ntt=1 unless you are sure you know what you
are doing." (This is especially true for implicit solvent simulations.)

Your mileage may vary, but I almost never use ntt=1 anymore.

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