[gmx-users] g_rmsf

[Efrat Noy]

Hi,

I have 2 questions regarding root mean square fluctuation calculations:

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? 

2. Is it possible to fit the trajectory structures, prior to rmsf calculations, on only part of the protein?

Thanks, Efrat
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