AMBER Archive (2006)

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

From: Tanya Johannsen (tanyajohannsen_at_yahoo.com)
Date: Fri Nov 03 2006 - 18:38:38 CST

Thank you for your reply. One question: does the use of ntt=3 for simulated annealing (and hence high temperatures) affect how I should define gamma_ln? Based on tutorials and the literature that I've looked at I thought that gamma_ln=1.0 was a pretty reasonable choice for room temperature simulations. However, in the only tutorial that I've been able to find that uses ntt=3 for simulated annealing (http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_seven/section5.htm), gamma_ln is equal to 1000.0. Does this have something to do with the high temperatures? I have consulted the literature and it is not clear to me how gamma_ln should be affected (if at all) by performing simulated annealing
  rather than a room temperature simulation. I would be very grateful if anyone could offer their suggestions on defining gamma_ln.
   
  Thank you in advance.
   
  Tanya
  

Carlos Simmerling <carlos_at_csb.sunysb.edu> wrote:
  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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