[gmx-users] part of ligand molecule leaves protein

[Gaurav Goel]

Dear Andrew:

You can look at temporal profile of area buried at the protein-ligand
interface / protein-ligand coordination number. If there is a sharp change
at the beginning of simulation it might be indicative of improper
equilibration of complex. A gradual change over initial few nanoseconds
would imply that the starting complex is not even metastable.

Regards,
Gaurav

Gaurav Goel, PhD
Associate Professor
Department of Chemical Engineering
Indian Institute of Technology, Delhi
Hauz Khas, New Delhi 110016
India


On Thu, Jul 11, 2019 at 11:40 AM Andrew Bostick <andrew.bostick1 at gmail.com>
wrote:

> Hi gromacs users,
>
> I did md simulation of the protein-ligand complex.
>
> As shown in figure, after 50 ns, part of ligand molecule leaves protein. I
> remind that I resolve pbc problem at first.
>
> https://1drv.ms/u/s!AveJH4Y30cH0tFp_XYCqkrCd7Kqq
>
> What is the reason of this state?
>
> Best,
> Andrew
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