AMBER Archive (2007)

Subject: AMBER: The convergence criteria for the energy minimization of the DNA molecule (dodecmer duplux)

From: Chengwen Chen (chenchengwen_at_gmail.com)
Date: Fri Jan 19 2007 - 03:37:53 CST

Dear Sirs / Madams,

I am a Ph.D. student at Department of Chemistry, The Chinese University of
Hong Kong. The aim of my Ph.D. project is to stimulate the DNA molecule
using Amber. When I want to get an optimized structure of the DNA molecule,
I find that there is no convergence crtieria implemented in the program. I
have no idea how to determine the convergence criteria. For example, what
is the energy difference between DNA structures searched for the convergence
criteria? Are there any other parameters used for the convergence criteria?

Thank you for your help and attention.

Regards,

Wendy Chen

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