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

silvester.thu silvester.thu at gmail.com
Fri Apr 25 13:31:15 CEST 2008

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!


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: Mark Abraham
发送时间: 2008-04-25 19:11:14
收件人: Discussion list for GROMACS users
主题: Re: [gmx-users] negative eigenvalues occured and not "nearly zero"

silvester.thu  wrote:
>  Hi  Berk,  thanks  for  your  reply,  but  there  are  still  problems.
>  While  the  first  six  eigenvalues  are  corresponding  to  the  three  
>  translational  and  three  rotational  dimensions  of  freedom  of  the  whole  
>  system,  they  should  be  zero  (theoretically)  or  at  least  not  
>  much  different  from  zero  (e.g:  1e-3  or  -1e-3).  But  in  my  problem,  I  
>  encountered  some  negative  values  that  are  much  different  from  zero,  as  I  
>  listed  before.  
>  And  I  have  used  the  g_nmtraj_d  to  generate  and  visualize  the  modes  
>  corresponding  to  those  negative  eigenvalues,  and  I  found  that  those  
>  modes  were  neither  translational  nor  rotational  movements  --  they  were  
>  actually  "oscillational  movements".  It  is  unreasonable.  So  I  guess  there  
>  might  be  something  wrong  in  my  calculation.  But,  I  still  can  not  figure  
>  out  what  is  wrong,  even  after  I  discussed  with  members  in  my  group  this  
>  morning.

I  don't  have  much  experience  in  such  a  calculation  with  an  MM  force
field,  but  such  Hessian  eigenvalues  in  quantum  chemistry  indicate  that
you  are  at  some  non-minimum  stationary  point.  That  seems  unlikely  for  an
MM  EM  calculation,  unless  the  PES  is  very  flat.  I  can't  guess  what
"oscillational  movements"  are,  but  if  you  perturb  the  system  in  the
direction  of  that  eigenvector  (easy  if  it's  mostly  on  a  few  atoms,
otherwise  just  add  a  suitable  multiple  of  the  eigenvector  to  the  atom
coordinate  vector)  you  can  see  if  you  get  into  the  range  of  a  suitable
local  minimum,  or  return  to  your  existing  stationary  point.

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