From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Wed Oct 27 2010 - 03:12:08 CDT
I use this script<http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/fitframes/>to
align all frames with the first. This effectively removes translation
rotation of the protein.
On Wed, Oct 27, 2010 at 09:39, divya nayar <divya.alchemist_at_gmail.com>wrote:
> 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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