[gmx-users] Decreasing MSD of ligand ?

[Justin A. Lemkul]

Chih-Ying Lin wrote:
> Hi
> The MSD decrease occurs in the long times.
> The ligand has bounded to a protein.
> How can the decrease happen?
> 

Probably because the ligand, being bound to the protein, has its motion 
restricted by its interaction with the protein.  I don't see the purpose of 
measuring the MSD of a bound compound, since it probably shouldn't change much, 
anyway, if the ligand remains in the active site.  MSD is much more useful for 
measuring the movement of more freely-diffusible entities (solvents, lipids, etc).

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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