[gmx-users] question about xaver.pdb from g_rmsf

Marc Baaden baaden at smplinux.de
Sat Oct 11 16:38:01 CEST 2003


could somebody give some details on how the average coordinates
in xaver.pdb (generated via g_rmsf -ox) are calculated ? I have
compared with a homewritten perl script that calculates the average
by equally averaging all frames.

If I only analyze the coordinates of a single frame, the result is

For any bigger number of frames there is a deviation.

I have verified my perl script (by re-calculating the averages by
hand), and it is correct, eg does the simple average weighting
every frame the same (ignoring time information).

What does g_rmsf do differently ?

Thanks in advance,

 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:baaden at smplinux.de      -      http://www.marc-baaden.de
 FAX: +49 697912 39550  -  Tel: +33 15841 5176 ou +33 609 843217

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