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No Access Submitted: 18 September 1995 Accepted: 29 March 1996 Published Online: 31 August 1998

  • Simulation of activation free energies in molecular systems

J. Chem. Phys. 105, 1902 (1996); https://doi.org/10.1063/1.472061
Eyal Neria
  • Department of Chemistry, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
    • Stefan Fischer and Martin Karplus
  • Department of Chemistry, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138
  • Laboratoire de Chimie Biophysique, Institut Le Bel, Universite Louis Pasteur, 4 rue Blaise Pascal, Strasbourg, France 67000
    • more...View Contributors
    • Eyal Neria
    • Stefan Fischer
    • Martin Karplus
    ABSTRACT
    A method is presented for determining activation free energies in complex molecular systems. The method relies on knowledge of the minimum energy path and bases the activation free energy calculation on moving along this path from a minimum to a saddle point. Use is made of a local reaction coordinate which describes the advance of the reaction in each segment of the minimum energy path. The activation free energy is formulated as a sum of two terms. The first is due to the change in the local reaction coordinate between the endpoints of each segment of the path. The second is due to the change in direction of the minimum energy path between consecutive segments. Both contributions can be obtained by molecular dynamics simulations with a constraint on the local reaction coordinate. The method is illustrated by applying it to a model potential and to the C7eq to C7ax transition in the alanine dipeptide. It is found that the term due to the change of direction in the reaction path can make a substantial contribution to the activation free energy.

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