[gmx-users] g_rmsf -res bug

Marco Pasi mfpasi at gmail.com
Fri Apr 20 14:37:55 CEST 2007

Hi all,

I was looking at the output of various g_rmsf runs, and came upon the fact that
the RMSF values obtained using -res and then choosing Mainchain (5)
for RMS calculation, were exactly the same as the RMSF values of
Mainchain Oxygen atoms obtained not using -res.  I gave a look at the
code to see why this was the case, and discovered that the averaging

[src/tools/gmx_rmsf.c lines 355-356]
  if (bRes) {

is done before the rmsf array is filled with the values from the U
tensors.  Thus the values output by g_rmsf are the RMSF values of the
last atom of each residue (and not the average of the residue), and in
the case of the Mainchain, Oxygen.

The attachment is a simple patch for src/tools/gmx_rmsf.c (v 1.3,
GROMACS 3.3) that solves the problem.



Marco Pasi, PhD Student
Department of Biotechnology and Biosciences
University of Milan-Bicocca
Piazza della Scienza, 2
20126 Milan - Italy
Phone: +39.02.64483475
E-mail: marco.pasi at unimib.it
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