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Hi Berk,<br>
<br>
I'm using NMA - sorry I didn't mention it before.<br>
<br>
Thanks,<br>
Ran.<br>
<br>
Berk Hess wrote:
<blockquote cite="mid4A366A4D.5000803@cbr.su.se" type="cite">
<pre wrap="">Ran Friedman wrote:
</pre>
<blockquote type="cite">
<pre wrap="">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
</pre>
</blockquote>
<pre wrap=""><!---->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
</pre>
</blockquote>
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