[gmx-users] negative eigenvalues occured and not "nearly zero"

silvester.thu silvester.thu at gmail.com
Fri Apr 25 15:04:41 CEST 2008

Hi Berk,

I am working on a system of graphenes. As the topology of graphite is known and simple, I assume that the system can reach a very low energy level. However, I still not know how to minimize the energy of such a system containing protein to Fmax<1e-9, as the description I quoted before.  Or did I misunderstand the description of that author I mentioned before?
So, could the graphene system I am working on reach such a low energy level like 1e-9? I have tried every way I can figure out, but they did not work.
By the way, I used CG integerator.

Thanks for your attention!

With my best regards.

Yue Shao



Shao Yue
Institue of Biomechanics and Biomedical Engineering
Department of Engineering Mechanics
Tsinghua University
P.R. China

发件人: Berk Hess
发送时间: 2008-04-25 20:38:25
收件人: Discussion list for GROMACS users
主题: RE: [gmx-users] negative eigenvalues occured and not "nearly zero"

Date: Fri, 25 Apr 2008 19:31:15 +0800
From: silvester.thu at gmail.com
To: gmx-users at gromacs.org
Subject: Re: Re: [gmx-users] negative eigenvalues occured and not "nearly zero"

Thanks Mark. 
I also have doubted that the system was not at the minium stationary point before, because I searched the mailing-list archive and found the description below:

I have checked the first eigenvalues in .xvg files, some of them really large.
For example, a 88 amino acid protein (PDB ID=1krn), there are 79 amino 
acid coordinates in the PDB file. After EM, the Max force< 1e-9, while the
first 12 eigenvalues g_nmeig_d worked out are:
     1     0.000438558
     2    -0.000683771
     3     -0.00292664
     4      0.00597364
     5      0.00817211
     6      -0.0114438 
     7         1.58334
     8         1.80916
     9         2.04356
    10          2.6188
    11         2.87512
    12         3.44095

The author of this description was describing another problem which was different from my question. But this descripment is helpful for me. In this description, the author minimized the energy of the system to reach the level -- Fmax<1e-9 -- which I do not know how to get to. I have tried my best to EM, but I only got Fmax<3e-4. In the mdrun_d step, there is no warning, while in the g_nmeig_d step, there is a warning that 

One of the lowest 6 eigenvalues has a non-zero value.
This could mean that the reference structure was not
properly energy minimized.

So the system may be not at the minimum stationary point. How can I make the system to reach this point?

What's more, in the description above, the first six eigenvalues are very near to zero, and that is what I want now, because as I said before, I can not get such "nearly zero" eigenvalues.

So, if you know how to do the EM to such a low energy level, or how to get those "nearly zero" eigenvalues, please give me some advice or some examples.

Thanks a lot for your attentions!

I assume you are already using CG or LBFGS.

You did not describe your system, but if you for instance have water molecules around
a protein, it becomes very difficult to minimize to low forces.


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