[gmx-users] PROTEIN FOLDING

[Vytautas Rakeviius]

Yes, you can open all structural output files with VMD. Or Chimera (tools MD so on).
 

    On Thursday, April 6, 2017 9:56 AM, Neha Gupta <nehaphysics17 at gmail.com> wrote:
 

 Hi gromacs users,


I have run 2ns simulation of protein ligand complex using NVT ensemble
(after equilibration).


I want to know whether there is a structural/conformational change in the
protein especially in the active site where, the ligand forms hydrogen
bonds with the protein during simulation.


Can we visualize it? Is it possible?

Please let me know.


Thanks,
Neha
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