Re: Energy minimization in NAMD

From: Ajasja Ljubetič (
Date: Tue Aug 09 2016 - 04:24:08 CDT


Your system is stuck in a local minimum/saddle. Local minimization methods
(such as conjugated gradient etc...) will not help you get out of the local
minimum. You can try to heat up the system and cool it down again. This is
called simulated annealing
<> and may help you cross
from the local to the global minimum.

Alternately you can very the dihedral angles of your molecule, so that you
start local minimization from different conformations, one of which will
hopefully converge to the global minimum.
Although rigorously proving that you have found the global minimum is also

Good luck,

On 8 August 2016 at 23:42, Faramarz Joodaki <> wrote:

> Dear Ajasja,
> Thank you for your email!
> Unfortunately, I did not get your idea! Could you please explain a little
> more?
> Best Regards,
> Faramarz
> On Mon, Aug 8, 2016 at 4:54 PM, Ajasja Ljubetič <
> > wrote:
>> Hi!
>> You could try simulated annealing
>> <>
>> or simply generating large amounts of starting conformations far apart and
>> minimizing them all.
>> Best,
>> Ajasja
>> 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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