From: Faramarz Joodaki (fjoodaki_at_my.uri.edu)
Date: Mon Aug 08 2016 - 11:37:45 CDT
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.
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