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<P>Hi,
<P>I have 2 questions regarding root mean square fluctuation calculations:
<P>1. what exactly is the difference between the values in the rmsf.xvg file and
the values in the rmsdev.xvg file (obtained with the -od
option)? Are the rmsf.xvg values are standard deviations of atom
positions along the trajectory with respect to an average structure
of the trajectory? And rmsdev.xvg values are the same but in respect
to a reference structure defined by the tpr file?
<P>2. Is it possible to fit the trajectory structures, prior to rmsf
calculations, on only part of the protein?
<P>Thanks, Efrat</P></FONT></DIV></BODY></HTML>