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

[Khadija Amine]

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*