A minimal implementation of the AMBER–GAUSSIAN interface for ab initio QM/MM-MD simulation
✍ Scribed by Takuya Okamoto; Kenta Yamada; Yoshiyuki Koyano; Toshio Asada; Nobuaki Koga; Masataka Nagaoka
- Publisher
- John Wiley and Sons
- Year
- 2010
- Tongue
- English
- Weight
- 1017 KB
- Volume
- 32
- Category
- Article
- ISSN
- 0192-8651
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✦ Synopsis
Abstract
For applying to a number of theoretical methodologies based on an ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics method connecting AMBER9 with GAUSSIAN03, we have developed an AMBER–GAUSSIAN interface (AG‐IF), which can be one of the simplest architectures. In the AG‐IF, only a few subroutines addition is necessary to retrieve the QM/MM energy and forces, obtained by GAUSSIAN, for solving a set of Newtonian equations of motion in AMBER. It is, therefore, easy to be modified for individual applications since AG‐IF utilizes most of those functions originally equipped not only in AMBER but also in GAUSSIAN. In the present minimal implementation, only AMBER is modified, whereas GAUSSIAN is left unchanged. Moreover, a different method of calculating electrostatic forces of MM atoms interacting with QM region is proposed. Using the AG‐IF, we also demonstrate three examples of application: (i) the QM versus MM comparison in the radial distribution function, (ii) the free energy gradient method, and (iii) the charge from interaction energy and forces. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011