From: Leandro Martínez (leandromartinez98_at_gmail.com)
Date: Sat Feb 03 2007 - 06:35:32 CST
You cannot guarantee also that any simulated-annealing scheme
will not be trapped in a local minimum. Such thing as a practical algorithm
that guaranteedly converge to a global minimum do not exist. Such
algorithm would be a mayor breaktrhrough for protein modeling.
Leandro.
On 2/3/07, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>
> Hi Shirley,
> minimization in the MD context is by nature local and not global. The
> very purpose of the minimization is to seek a local minimum so that you
> can start your simulation from a stable point. Once you start dynamics
> you'll pop out of it fast enough...
> Peter
>
> Shirley Hui wrote:
> > Hello,
> >
> > I wanted to know if it is possible to perform energy minimizations in
> > NAMD using a simulated annealing approach? The manual seems to
> > indicate that NAMD is only able to perform minimization using:
> >
> > Conjugate gradient approoach or
> > Velocity quenching scheme
> >
> > How do you ensure the algorithm isn't trapped in a local minimum?
> >
> > Thanks
> > shirley
>
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