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Role of a reaction coordinate in free energy calculations |
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| Authors: | Styliani Consta Anatoly Malevanets Myong In Oh Mahmoud Sharawy |
| Affiliation: | 1. Department of Chemistry, The University of Western Ontario , London, Canada.sconstas@uwo.ca;3. Department of Electrical &4. Computer Engineering, The University of Western Ontario , London, Canada.;5. Department of Chemistry, The University of Western Ontario , London, Canada. |
| Abstract: | AbstractThe free energy calculation method emerges as a viable technique for ‘in-silico’ calorimetry. Efficient sampling techniques and the good choice of a reaction path connecting the reactant and the product state enable accurate computations of the free energy differences. We argue that in many cases the thermodynamic integration technique has the lowest variance when the transformation between the reactant and the product state proceeds along the natural path of the studied chemical reaction. We provide examples of free energy calculations for the fragmentation of the charged clusters and the swapping reaction of oligomer formation in proteins that follow a tentative reaction mechanism. |
| Keywords: | Multiple replica repulsion method cluster fragmentation protein oligomerisation mechanism domain swapping |