[gmx-users] Molecular dynamic simulations of Protein-DNA complex

[Khadija Amine]

Hello Erik,

Thank you.

I mean that the global shape of the complex is lost from 5ns to 10ns.
After that, the structural flexibility of the complex is regained.





*Khadija AMINE*


*Computational Biology*
*Postdoctoral Research Associate*
*Carnegie Mellon University*

On Mon, Oct 24, 2016 at 11:06 AM, Khadija Amine <kh.amine1 at gmail.com> wrote:

> Dear Gromacs users,
>
> I have run 20ns of MD simulations of my protein-DNA complex.
>
> All my trajectory files have been combined in a same final file.
>
> I have visualized that trajectory file using pymol software.
> Unfortunately, the DNA structure and some parts of the complexed protein
> structure show deformations.
>
> How can I prevent this issue and obtain correct structure, movement of my
> complex?
>
> This is the first time I perform MD for the protein - DNA complex.
>
> Thank you
>
> *Khadija AMINE*
>
>
> *Computational Biology*
> *Postdoctoral Research Associate*
> *Carnegie Mellon University*
>