[gmx-developers] rmsf units in g_anaeig

Ran Friedman r.friedman at bioc.uzh.ch
Mon Jun 15 17:00:21 CEST 2009

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
The eigenvectors are normalized by u-1/2 so:
should give units u-1

the units of sqrtm seem to be u-1/2.

but the rmsf units should be nm

What am I missing?


Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355559
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman

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