[gmx-users] Representative structure of a long simulation

Marc Baaden baaden at smplinux.de
Mon Apr 29 14:32:44 CEST 2002

Hi there,

thanks a lot for all those useful comments about my query.
I will start trying these approaches, but some comments beforehand:

- Nobody considered an energy criterium as discrimination possibility
 (although Y. U. Sasidhar mentioned that the most populated conformation
  should be representative).
  Why ? Isn't it that in principle the frame with minimum energy should
  be the one which will (statistically in the long term) be the most
  populated ? I agree, that being interested in just a protein structure
  leads to the question as to which energy has to be used (as the whole
  system contains other components, too), but it seemed a canonical
  choice to me.

Berk Hess said:
>> My suggestion would be to perform a covariance analysis [..]
>> For large (membrane) proteins convergence can be a problem.

I agree, but the spirit of my question was more: let's forget about
sampling issues and assume I have the structures in this trajectory,
and just based on this trajectory which would be the one most representative
for the sampled region of phase space.

dbostick at physics.unc.edu said:
>> This may seem too simple for you, but if I were looking for a
>> "representative" structure of a protein, I would just take the time
>> averaged structure.

No, it's not too simple, but as has been pointed out by Anton Feenstra
and Y. U. Sasidhar, this average structure is not one of the snapshots,
but might be an unphysical structure in terms of bond lengths, etc.
This I wanted to avoid.


 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
 mailto:baaden at smplinux.de  - ICQ# 11466242 -  http://www.marc-baaden.de
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