global and internal motion of protein

From: divya nayar (
Date: Wed Oct 27 2010 - 02:39:04 CDT

I am doing MD simulation of solvated protein system. I am calculating the
Mean squared-displacements of heavy atoms of protein. I want to know how can
I remove the global motion of protein in order to get the internal motion of
protein? Can NAMD do so? and what does it mean by internal motion of protein
because I am not keeping my protein flexible during simulation.


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