[gmx-users] Decreasing MSD of ligand ?

[Justin A. Lemkul]

Chih-Ying Lin wrote:
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> HI MSD = mean square displacement diffusion coefficient = d/dt (MSD) I 
> simulate the protein and ligand system and then calculate the MSD of the 
> ligand. Then, i drew the plot of the time evolution of the MSD. But the 
> the MSD decreases as time for some period. I see nothing about my 
> codings. Would you please tell me about any possible errors i made? 

MSD can decrease due to insufficient sampling (time of the simulation, number of 
frames analyzed, etc).  Depending on what you define as "some period" (during 
the initial part of the simulation? the middle? the end?) the behavior may or 
may not be normal, but from the few details you provide, there's no way to know. 
  What do you hope to see in this analysis?  Will a ligand bound to a protein 
really diffuse that much anyway?

-Justin

> Thank you Lin
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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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