Re: Energy minimization

From: Aron Broom (
Date: Tue Aug 16 2016 - 09:57:04 CDT

are you doing energy minimization or dynamics? you say here 1 ns and talk
about time-steps, that sounds like dynamics. Energy minimization would
just be steps, one can't really assume any particular time.

Assuming it really is minimization, I think you should expect a continuous
decrease in energy over time. I don't really see why it would need to be
straight. Maybe I'm missing something, can you explain why you think it
ought to be straight?

On Mon, Aug 15, 2016 at 1:05 AM, <> wrote:

> In my models used for energy minimization in NAMD, after 1ns i.e., 1000000
> time-steps. I am not getting a completely straight line. Is it compulsary
> to get a totally straight line in the energy minimization step? what are
> the reasons for not getting a completely straight line?

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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