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

[Quin K]

Hi All,

Further to following email, i just noted that the ligand has detached from
binding site.
Is there a way to prevent this from happening?
It happened to me once before with the same complex.
Doesn't boundary conditions prevent ligand from detaching from binding site
in protein during MD simulation?
Your advice needed.

Thank you in advance!

On Sun, Dec 15, 2019 at 8:12 PM Quin K <profiles.ke at gmail.com> wrote:

> Hi
>
> During RMSD analysis of protein ligand complex I got the following graph.
> RMSD of how much the ligand position has varied relative to the protein is
> given in the graph (Please see the link below).
>
>
> https://drive.google.com/file/d/1rvkHYisjmjFDvN6Lldo5Gejz7nJKEKnl/view?usp=sharing
>
> I noted that there is a lot of variation in the graph. Is this normal?
> Should I continue with the simulation for 100 ns? Or should I redo the
> simulation all over?
>
> Thank you
> Regards
>