[gmx-users] RMSD analysis of protein-ligand complex

[Justin Lemkul]

On 10/5/19 11:59 AM, Quin K wrote:
> Thank you.
>
> I got following when I analysed Ligand RMSD protein backbone as east square
> fit.
> Graph <https://photos.app.goo.gl/JZJaLt1BxJi1qgwV7>
> Can you please comment why there's high fluctuation after like 23 ns?
> What could this mean?

Watch the trajectory and see what is going on. Make sure you've properly 
re-imaged to account for PBC effects.

-Justin

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Justin A. Lemkul, Ph.D.
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