[gmx-users] Normal mode eigenvalue units, nm^-2 ??
baaden at smplinux.de
Thu May 19 17:21:48 CEST 2005
>>> "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
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 ). Maybe the author's statement "[..] the lowest 3 quasiharmonic
modes are due to irreversible transitions between conformational substates
(structural drift)[..]" reflect exactly this.
 "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
FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217
More information about the gromacs.org_gmx-users