AMBER Archive (2009)

Subject: [AMBER] The decreasing MSD of ligand??

From: Chih-Ying Lin (chihying_at_usc.edu)
Date: Wed Nov 18 2009 - 15:19:35 CST

Hi
The ligand has bound to the protein.
and at some period of time, the MSD of the ligand decreased.

Any ideas about this?

Thank you
Lin

----- Original Message -----
From: Chih-Ying Lin <chihying_at_usc.edu>
Date: Tuesday, November 17, 2009 11:07 am
Subject: [AMBER] MSD of ligand??
To: AMBER Mailing List <amber_at_ambermd.org>

>
>
> 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?
> Thank you
> Lin
>
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