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

Berk Hess gmx3 at hotmail.com
Thu May 19 16:03:11 CEST 2005

>From: Marc Baaden <baaden at smplinux.de>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] Normal mode eigenvalue units, nm^-2 ?? Date: Thu, 
>19 May 2005 15:56:04 +0200
> >>> "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
>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 ?

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.

>  >> 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).

Indeed, I overlooked the -ol option.

>Maybe -of/-ol would also be useful for g_covar (re: comments above)

See my comment above.


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