CHARMM free energy methods

We describe interatomic interactions using the functional form U q) dehned by the CHARMM 27 force field, a standard force field available in many biomolecular-oriented molecular dynamics codes. For the sake of simplicity, all the simulations are carried out in vacuum as the free-energy landscape in such conditions presents several interesting features and has been studied previously using many different free-energy methods (see, e.g.. Refs. 30-35) thus being a perfect test bed for the discussion. 

In this approach, the coexistence oi both solute molecules in the presence a common solvent environment is required. Applying the AMl(MNDO)/ CHARMM potential, the free energy of activation for the 5 2 reaction, Cl + CH3CI - CICH3 + Cl, was computed and found to be in good agreement with experiment and previous theoretical data. > The method has been successfully used in classical molecular dynamics simulation of proteins in aqueous solution.1 8-151... 

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