From: d.ronika_at_iitg.ernet.in
Date: Wed Aug 17 2016 - 05:09:01 CDT
I do not understand what you meant by blow apart. Can you please explain
why do we actually do minimization?
> From what I understood, you mean that his minimization seems to not have
> converged even after 1.000.000 steps. This is somewhat untypical but may
> be related to your system. Can u explain what your system consists of?
> But, btw. you don’t need a fully converged minimization if you plan to
> do molecular dynamics afterwards, since the minimization usually has the
> purpose, just to remove initial conditions that would blow apart the
> system otherwise.
>
>
>
> Norman Geist
>
>
>
>
>
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
> von Aron Broom
> Gesendet: Dienstag, 16. August 2016 16:57
> An: namd-l_at_ks.uiuc.edu; d.ronika_at_iitg.ernet.in
> Betreff: Re: namd-l: Energy minimization
>
>
>
> 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, <d.ronika_at_iitg.ernet.in
> <mailto:d.ronika_at_iitg.ernet.in> > 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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