[gmx-developers] rmsf units in g_anaeig

Ran Friedman r.friedman at bioc.uzh.ch
Mon Jun 15 17:57:05 CEST 2009

Hi Berk,

I'm using NMA - sorry I didn't mention it before.


Berk Hess wrote:
> Ran Friedman wrote:
>> Hi All,
>> I was looking at the gmx_anaeig code to see how it calculates the rmsf
>> for each vector.
>> At function rmsf, I find:
>> (GMX 4.04, lines 713-714):
>>       for(i=0; i<natoms; i++)
>>           y[g][i] = sqrt(eigval[eignr[v]]*norm2(eigvec[v][i]))/sqrtm[i];
>> The units of the eigenvalues are kJ mol-1 nm-2 u-1
> How did you get to this unit?
> g_covar generates eigenvalues with the unit nm^2 u, if you use mass
> weighting.
> If you don't use mass weighting, all the mass units disappear.
> Or are you using a matrix from a normal mode analysis?
> In that case I think it is not useful to look at rmsf, you could simply
> look at the vector components.
> Berk

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