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

[Marc Baaden]

>>> "Berk Hess" said:
 >> As eq 3.66 says, it is a frequency to the power -2. The unit is ps^-2
 >> for mass-weighted, amu ps^-2 for non mass weighted.

Ok, thanks. Makes things a lot clearer. Leads to a conversion of
5.309 cm-1 * sqrt(gmx_eigenval) to wavenumbers, if I got the numbers
right.

If I wanted to compare the frequency spectrum of a normal mode calculation
to results from principle components analysis of an MD simulation, would it
be sufficient to use g_covar with mass-weighting (-wma) to actually do a
quasi-harmonic analysis, or is there something else that needs to be done ?


 >> In the CVS code it is cm^-1, which is written in the xvg file.

This is for the -of option I guess (which didn't exist in 3.2.1).
Maybe -of/-ol would also be useful for g_covar (re: comments above)


Now I set out to use the CVS version, but I get the warning:
> Fatal error:
> No matrix data found in file. Note that the Hessian matrix format changed
> in Gromacs 3.3 to enable portable files and sparse matrix storage.

So I wonder whether there is a way to convert (or otherwise use) the
previously calculated hessian's (mtx files) ?

Thanks,
Marc

-- 
 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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