A Comparison of Non-Bonded Scaling Approaches for Free Energy Calculations

Authors: Pitera J.W.¹; van Gunsteren W.F.¹

Source: Molecular Simulation, Volume 28, Number 1, 1 January 2002 , pp. 45-65(21)

Publisher: Taylor and Francis Ltd

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Abstract:

One of the long-standing problems in free energy calculations that involve the annihilation of particles is the choice of how to scale the non-bonded interactions of the disappearing particle. We make use of a "null transformation" (converting naphthalene to naphthalene) to extensively test and compare a number of scaling approaches, including simple linear, quadratic, mixed non-linear and separation-shifted ("soft-core") scaling. While any protocol that involves some sort of non-linear scaling yields reasonable free energy results, only the "soft-core" scaling methods yield completely stable dynamics near the simulation end-points. Additional advantages of this method in the context of complex molecular conversions are also discussed.

Keywords: Free energy calculations; Molecular dynamics; Thermodynamic integration; Non-bonded interactions; End-point catastrophe

Document Type: Research article

Affiliations: 1: Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH Zürich, ETH Zentrum, CH-8092, Zürich, Switzerland

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