A versatile AMBER-Gaussian QM/MM interface through PUPIL

作者：Torras Juan^*; Seabra Gustavo De M; Deumens Erik; Trickey S B; Roitberg Adrian E

来源：Journal of Computational Chemistry, 2008, 29(10): 1564-1573.

DOI：10.1002/jcc.20915

• 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.

• 出版日期2008-7-30