AMBER Archive (2006)

Subject: Re: AMBER: Performing Simulated Annealing?

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Fri Apr 28 2006 - 12:16:43 CDT

you can either put in multiple weight change cycles in the sander input,
or write a small script for your script to run sander several times.
keep in mind that cycles of warming/cooling is a lot like doing
replica exchange, so you might want to read more about that if you
haven't already.

alfredoq_at_fcq.unc.edu.ar wrote:

>Dear Amber community:
>
>I am trying to perform a conformational search using a molecular dinamic
>simulted annealing aproach. I have created the input file for sander in order
>to perform 1 cycle of the whole process. I was wondering if there is any
>keyword to repeat the warming-cooling cycle n times. After this, I guess I am
>supposed to perform a manual cluster analysis over the whole trajectory to
>extract the conformation ensembles?
>Thanks in advance for the help
>Best wishes
>
>Alfredo Quevedo
>
>
>
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