[gmx-users] Decreasing MSD of ligand ?

Chih-Ying Lin chihying2008 at gmail.com
Wed Nov 18 22:16:16 CET 2009

The MSD decrease occurs in the long times.
The ligand has bounded to a protein.
How can the decrease happen?

Thank you

Chih-Ying Lin wrote:
> 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"
the initial part of the simulation? the middle? the end?) the behavior may
may not be normal, but from the few details you provide, there's no way to
 What do you hope to see in this analysis?  Will a ligand bound to a protein
really diffuse that much anyway?


> Thank you Lin
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