ISSN:
1089-7690
Source:
AIP Digital Archive
Topics:
Physics
,
Chemistry and Pharmacology
Notes:
A new method of using multiple potential functions (mutation bases) in free energy perturbation calculations is proposed to make more effective mutation pathways. The method, which is a generalization of the conventional coupling parameter approach, allows pathways of more freedom and of smoothly curved shapes to be produced. Molecular dynamics simulations were carried out by the method to derive relative free energy on a model system made of 64 four-atom molecules in the periodic boundary condition. Effectiveness of five mutation pathways was compared using the resulting free energy values and the final ratios of trans conformations. For confidence, 15 free energy perturbation calculations were carried out for each shape and length of the mutation pathways, and means and standard errors were calculated. Results showed that one of the pathways, which is impossible without the multiple mutation bases, is more effective than the down-scaled pathway proposed by Mark et al. [J. Chem. Phys. 94, 3808 (1991)], and is much more effective than the simple mutation of the conventional coupling parameter approach.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1063/1.463650
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