Re: global and internal motion of protein

From: Ajasja Ljubetič (
Date: Wed Oct 27 2010 - 03:12:08 CDT

I use this script<>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 <>wrote:

> Hi,
> 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.
> Thanks,
> Divya

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