AMBER: Simulated Annealing - Start with Poor Structure

From: Seth Lilavivat <>
Date: Tue, 22 May 2007 15:28:54 -0400

Dear Amber Community,

Simulated annealing: many of you have commented that a poor initial structure
can be the cause of many problems. However, I noticed that several papers
document that they started with extremely irregular random structures by
performing high temperature MD (as high as 4000K), unrestrained. I am following
this protocol of running a short MD run at high temp to create a random starting
structure. My algorithm is capable of producing a low energy structure that
satisfies all of the restraints but it doesn't always converge. My question is
this: when is it appropriate to start with a structure that you believe to be
close to the final structure and when do you start with a random "disordered"

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Received on Wed May 23 2007 - 06:07:41 PDT
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