AMBER Archive (2006)

Subject: Re: AMBER: ntt=1 in simulated annealing

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Fri Nov 03 2006 - 05:48:06 CST

you can use the weight changes to make gradual changes to TEMP0
and it will work fine. Check page 106 of the Amber9 manual and it
shows you how to do weight changes.

Tanya Johannsen wrote:

> Dear AMBER community:
>
> I am working on a simulated annealing run. My understanding was that
> ntt=1 is traditionally used for simulated annealing since it is
> possible to use the tautp parameter to induce slow and gradual
> temperature changes. However, I saw that in the AMBER 9 manual it says
> "Unless you are sure you know what you are doing, please don't use
> ntt=1!" If not using ntt=1, what is the best method to use in
> simulated annealing? My understanding is that ntt=3 leads to a
> relatively quick adjustment to the target temperature, so even if I
> included many small adjustments in TEMP0, I'm concerned that it would
> be impossible to create a smooth temperature curve. I would appreciate
> any advice on the best choice for "ntt" in simulated annealing runs.
>
> Thank you in advance for any suggestions.
>
> Tanya
>
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