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

[Berk Hess]

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.

Berk.






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