[gmx-users] Normal mode eigenvalue units, nm^-2 ??

[Marc Baaden]

>>> "Berk Hess" said:
 >> That should work.
 >> But unless you simulate a very low temperature, I think this would
 >> not make sense for a protein, since the principal components with
 >> the largest eigenvalues are always diffusive at room temperature,
 >> not harmonic.

That's a very interesting aspect, I think. So what's your take then on
quasi-harmonic analysis for room temperature simulations (be it for entropy
estimation or comparison to NMA or ??) - should one remove the modes that
are diffusive and continue to work on the others or is there another general
flaw involved.

I wonder whether diffusion would show up as a mode that is not mainly
vibrational in character (in an analysis like that done at the end of
ref [1]). Maybe the author's statement "[..] the lowest 3 quasiharmonic
modes are due to irreversible transitions between conformational substates
(structural drift)[..]" reflect exactly this.

Marc Baaden

[1] "Harmonic Analysis of Large Systems. III. Comparison
with Molecular Dynamics." by Janezic, Venable & Brooks
Journal of Computational Chemistry 16(12): 1554-1568 (1995)

-- 
 BioMolSim meeting 2&3 Sep 2005: http://www.iecb.u-bordeaux.fr/satellite2005/

 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden at smplinux.de      -      http://www.baaden.ibpc.fr
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