Abstract
Electrostatic interactions play crucial role at various levels of biological systems. Being a long-range force, electrostatic force is known to be the major driving force for biomacromolecules interactions at long distance. Here, we developed a new molecular dynamics protocol named Electrostatic Force driven Molecular Dynamics (EFMD) simulation, which utilizes DelPhiForce along with NAMD molecular dynamics (MD) package. In EFMD the calculated electrostatic forces at each atom of the target are used in steered MD simulations. This protocol was applied to study the binding of substrates to protein receptor and to model protein-protein recognition. It is shown that EFMD greatly facilitates the success rate and reduces computational time.
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