A minimal implementation of the AMBER–GAUSSIAN interface for ab initio QM/MM‐MD simulation

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.

Comment on “a minimal implementation of the AMBER–GAUSSIAN interface for Ab Initio QM/MM‐MD simulation”

“…[1], ''We view that investment as largely a one-time cost which is fully justified by the relative ease and freedom from error in adding application packages later on.'' Recently, Okamoto et al [5] presented what they called a minimal implementation of an AMBER-GAUSSIAN interface.…”

“…Ref. [5] instead calculates the electric field at the positions of the MM particles via the GAUSSIAN ' 'Prop' ' option. In the course of their discussion, Okamoto et al make several other remarks about the design goals and the learning curve of PUPIL.…”

“…This conversion was made publicly available with the release of PUPIL 1.3 in December 2009, substantially prior to when Ref. [5] Unfortunately, the status of PUPIL as of the submittal date of Ref. [5] was mischaracterized.…”

“…[5] Unfortunately, the status of PUPIL as of the submittal date of Ref. [5] was mischaracterized. See, for example, the remark in Ref.…”

“…See, for example, the remark in Ref. [5] beginning with ' 'In the well-used…' ' This remark suggests that use of cubegen is intrinsic to PUPIL. Clearly it is not, as shown by the fact that cubegen is no longer required to run GAUSSIAN as a PUPIL user package.…”