期刊
JOURNAL OF COMPUTATIONAL CHEMISTRY
卷 29, 期 10, 页码 1564-1573出版社
WILEY
DOI: 10.1002/jcc.20915
关键词
multiscale simulations; hybrid QM/MM simulations; AMBER-PUPIL-GAUSSIAN interface; Angeli's salt; alanine dipeptide
The PUPIL package (Program for User Package Interfacing and Linking) originally was developed to interface different programs for multiscale calculations in materials sciences (Torras et al., J Comput Aided Mater Des 2006, 13 201; Torras et al., Comput Phys Commun 2007, 177, 265). Here we present an extension of PUPIL to computational chemistry by interfacing two widely used computational chemistry programs: AMBER (molecular dynamics) and Gaussian (quantum chemistry). The benefit is to allow the application of the advanced MD techniques available in AMBER to a hybrid QM/MM system in which the forces and energy on the QM part can be computed by any of the methods available in Gaussian. To illustrate, we present two example applications: A MD calculation of alanine dipeptide in explicit water, and a use of the steered MD capabilities in AMBER to calculate the free energy of reaction for the dissociation of Angeli's salt. (C) 2008 Wiley Periodicals, Inc.
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