[gmx-developers] rmsf units in g_anaeig

[Ran Friedman]

Hi Berk,

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

Thanks,
Ran.

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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