Grained Reactive Molecular Dynamics Algorithm

Coarse-Grained Reactive Molecular Dynamics Algorithm 

RMD is a generalized algorithm that can be used to describe any arbitrary chemical reaction in terms of three steps 

The RMD algorithm is implemented as an additional step at the end of each time step in a conventional MD simulation. Thus the interaction potentials used in the reactive simulation are non-reactive and are the same as those used to generate the membrane and interface morphologies described above. 

Once a reactant satisfies the complete set of triggers, the second step of the RMD algorithm is an instantaneous reaction where the reactants are replaced by products. In this way the information about the transition state from QM has been taken into account in step one but need not be explicitly included in step two. 

Instantaneous reactions are bound to disturb the system energetically and stractnrally. Thus, the third and final step is a local equilibration of the molecules participating in the reaction and those immediately adjacent. The purpose of the local equihbration is to re-estabhsh a reasonable stracture and satisfy the heat of reaction. Once the three steps of the RMD reaction are executed, the simulation proceeds to the next time step of the MD simulation. 

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Coarse-Grained Reactive Molecular Dynamics Algorithm... 

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