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

[Quin K]

Thank you.

I examined the trajectory using VMD and noted that ligand had come out of
the binding site and is running around.
How is this possible? I have used the guidelines in mdtutorials.com to set
up the system.
However it's worth noting that there was a power failure around the same
time (23ns) and I had to restart MD with append command.
Could this have had an affect on MD? Do I have to recreate trajectory file
after restarting MD, instead of using the default trajectory?

Regards

On Sat, Oct 5, 2019 at 9:53 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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.
> Assistant Professor
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