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

[Erik Marklund]

Dear Khadija,

Whether this is a real problem or not is not clear from what you have told us. It could be that what you see in the simulation is real, or it could be that the physical model is inadequate. Or you might even be reporting a visualisation artefact.

Can you please elaborate what you mean by “deformations”?

Kind regards,
Erik

> On 24 Oct 2016, at 10:06, 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*
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