A comparison of non-bonded scaling approaches for free energy calculations

被引：97

作者：

Pitera, JW ^{[1
]}

Van Gunsteren, WF ^{[1
]}

机构：

[1] Swiss Fed Inst Technol, ETH Zentrum, Swiss Fed Inst Technol, Phys Chem Lab, CH-8092 Zurich, Switzerland

来源：

MOLECULAR SIMULATION | 2002年 / 28卷 / 1-2期

关键词：

free energy calculations; molecular dynamics; thermodynamic integration; non-bonded interactions; end-point catastrophe;

D O I：

10.1080/08927020211973

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

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.

引用

页码：45 / 65

页数：21

共 34 条

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