MD simulation of Docked structures

User discussions
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1

GROMACS version: 2021.4
GROMACS modification: No

Hello,
I am new to running MD simulations on GROMACS, i need to do analysis of a 2 proteins docked in haddock.

I wanted to ask if the procedure will be same as in the Protein-Ligand tutorial.

I could not find any other resources concerning protein-protein MD simulation.

2

Running a simulation of a a protein complex is no different from running a simulation of a single protein. pdb2gmx can handle multiple chains in a single PDB file with no problem, as long as each chain has its own chain identifier or they are separated by TER cards.

3

Thank you sir