AMBER Archive (2007)

Subject: Re: AMBER: Simulated Annealing - Start with Poor Structure

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue May 22 2007 - 16:08:28 CDT

I start with leap-built extended structures or with high temperature
structures all the time. I don't run annealing but do run REMD on them
and don't really see problems. you do need to watch out for chirality
inversions and peptide bond isomerization, etc.

On 5/22/07, Seth Lilavivat <sethl_at_gatech.edu> wrote:
>
> 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"
> structure?
>
> Thanks,
> Seth
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