Re: Energy Minimization

From: Peter Freddolino (
Date: Fri Feb 02 2007 - 22:06:50 CST

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...

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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