QM/MM methods

A regularized and renormalized electrostatic coupling Hamiltonian for hybrid quantum-mechanical–molecular-mechanical calculations

The Journal of Chemical Physics, 123(16):164114-9.
P. K Biswas and V. Gogonea (2005)


We describe a regularized and renormalized electrostatic coupling Hamiltonian for hybrid quantum-mechanical (QM)–molecular-mechanical (MM) calculations. To remedy the nonphysical QM/MM Coulomb interaction at short distances arising from a point electrostatic potential (ESP) charge of the MM atom and also to accommodate the effect of polarized MM atom in the coupling Hamiltonian, we propose a partial-wave expansion of the ESP charge and describe the effect of a s-wave expansion, extended over the covalent radius rc, of the MM atom. The resulting potential describes that, at short distances, large scale cancellation of Coulomb interaction arises intrinsically from the localized expansion of the MM point charge and the potential self-consistently reduces to 1∕rc at zero distance providing a renormalization to the Coulomb energy near interatomic separations. Employing this renormalized Hamiltonian, we developed an interface between the Car-Parrinello molecular-dynamics program and the classical molecular-dynamics simulation program Groningen machine for chemical simulations. With this hybrid code we performed QM/MM calculations on water dimer, imidazole carbon monoxide (CO) complex, and imidazole-heme-CO complex with CO interacting with another imidazole. The QM/MM results are in excellent agreement with experimental data for the geometry of these complexes and other computational data found in literature.

URL: http://dx.doi.org/10.1063/1.2064907

A Hamiltonian electrostatic coupling scheme for hybrid Car–Parrinello molecular dynamics simulations

The Journal of Chemical Physics, 116(16):6941-6947.
Alessandro Laio, Joost VandeVondele, and Ursula Rothlisberger (2002)


We present a fully Hamiltonian and computationally efficient scheme to include the electrostatic effects due to the classical environment in a Car–Parrinello mixed quantum Mechanics/molecular mechanics (QM/MM) method. The polarization due to the MM atoms close to the quantum system is described by a Coulombic potential modified at short range. We show that the functional form of this potential has to be chosen carefully in order to obtain the correct interaction properties and to prevent an unphysical escape of the electronic density to the MM atoms (the so-called spill-out effect). The interaction between the QM system and the more distant MM atoms is modeled by a Hamiltonian term explicitly coupling the multipole moments of the quantum charge distribution with the classical point charges. Our approach remedies some of the well known deficiencies of current electrostatic coupling schemes in QM/MM methods, allowing molecular dynamics simulations of mixed systems within a fully consistent and energy conserving approach.

URL: http://dx.doi.org/10.1063/1.1462041

A hybrid method for solutes in complex solvents: Density functional theory combined with empirical force fields

The Journal of Chemical Physics, 110(21):10452–10467.
M. Eichinger, P. Tavan, J. Hutter, and M. Parrinello (1999)


We present a hybrid method for molecular dynamics simulations of solutes in complex solvents as represented, for example, by substrates within enzymes. The method combines a quantum mechanical (QM) description of the solute with a molecular mechanics (MM) approach for the solvent. The QM fragment of a simulation system is treated by ab initio density functional theory (DFT) based on plane-wave expansions. Long-range Coulomb interactions within the MM fragment and between the QM and the MM fragment are treated by a computationally efficient fast multipole method. For the description of covalent bonds between the two fragments, we introduce the scaled position link atom method (SPLAM), which removes the shortcomings of related procedures. The various aspects of the hybrid method are scrutinized through test calculations on liquid water, the water dimer, ethane and a small molecule related to the retinal Schiff base. In particular, the extent to which vibrational spectra obtained by DFT for the solute can be spoiled by the lower quality force field of the solvent is checked, including cases in which the two fragments are covalently joined. The results demonstrate that our QM/MM hybrid method is especially well suited for the vibrational analysis of molecules in condensed phase.

URL: http://dx.doi.org/10.1063/1.479049