From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Tue Aug 16 2016 - 23:53:20 CDT
>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.
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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