AMBER Archive (2006)

Subject: AMBER: ntt=1 in simulated annealing

From: Tanya Johannsen (
Date: Thu Nov 02 2006 - 21:44:19 CST

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.
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