A minimal implementation of the AMBER-GAUSSIAN interface for ab initio QM/MM-MD simulation.
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.
Okamoto
Takuya
T
Department of Complex System Science, Graduate School of Information Science, Nagoya University, Chikusa-ku, Nagoya, Japan.
Yamada
Kenta
K
Koyano
Yoshiyuki
Y
Asada
Toshio
T
Koga
Nobuaki
N
Nagaoka
Masataka
M
D056004:Molecular Dynamics Simulation; D011789:Quantum Theory; D013816:Thermodynamics