Re: Energy minimization in NAMD

From: Ajasja Ljubetič (
Date: Mon Aug 08 2016 - 15:54:58 CDT


You could try simulated annealing
or simply generating large amounts of starting conformations far apart and
minimizing them all.


On 8 August 2016 at 18:37, Faramarz Joodaki <> wrote:

> Hi everyone!
> I have done 10000 steps energy minimization on my system (1599 atoms).
> According to total energy plot and the amount of energy, I can state that
> the energy is stable. But I calculated the eigenvalues of the system (after
> minimization) and I found that some negative eigenvalues which it means
> that I am in the saddle point instead of global minimum. By changing the
> minimization parameters I could not reach the global minimum point. It is
> really important for me to reach that point for my next step research.
> I found also some parameters in the log file, which I do not know exactly
> what they mean:
> *DX, DU and DUDX.*
> In addition, I found that NAMD has just two methods for minimization. Is
> there any way to apply Newton-Raphson minimization method in NAMD?
> I would be so grateful if you could guide me with these matters.
> Best Regards,
> Faramarz

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