LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields

Abstract

We introduce an initial implementation of the LICHEM software package. LICHEM can interface with Gaussian, PSI4, NWChem, TINKER, and TINKER–HP to enable QM/MM calculations using multipolar/polarizable force fields. LICHEM extracts forces and energies from unmodified QM and MM software packages to perform geometry optimizations, single–point energy calculations, or Monte Carlo simulations. When the QM and MM regions are connected by covalent bonds, the pseudo-bond approach is employed to smoothly transition between the QM region and the polarizable force field. A series of water clusters and small peptides have been employed to test our initial implementation. The results obtained from these test systems show the capabilities of the new software and highlight the importance of including explicit polarization.

Computational Investigation of O2Diffusion Through an Intra–molecular Tunnel in AlkB; Influence of Polarization on O2Transport

“…65,66 AMOEBA combines distributed atomic multipoles (up to quadrupole) and (Tholé damped) inducible atomic dipoles, which have been shown to provide an accurate representation for various systems. 37,53,57,58,[67][68][69][70][71][72] Umbrella sampling/WHAM calculations for the AMOEBA calculations were performed using the amoebabio09 potential 73 using the same windows as for the ff99SB calculations. A harmonic potential (10 kcal mol −1 Å −2 , same as for the ff99SB PMF) was for each window.…”

Long-range electrostatic corrections in multipolar/polarizable QM/MM simulations

“…In practice [26], Eq. 2 can be expressed as $$H=H_{\text{qm}}^{\prime }+V_{\text{mm}}^{\prime }+V_{\text{mm},\text{pol}},$$ where $$H_{\text{qm}}^{\prime }=H_{\text{qm}}+V_{\text{qmmm},\text{mtp}},$$ and $$V_{\text{mm}}^{\prime }=V_{\text{mm}}+V_{\text{qmmm},\text{bnd}}+V_{\text{qmmm},\text{vdw}}.$$Here $H_{\text{qm}}^{\prime }$ adds the MM multipole moments ( V qmmm,mtp ) to the QM Hamiltonian, $V_{\text{mm}}^{\prime }$ adds the QM–MM bonded ( V qmmm,bnd ) and van der Waals ( V qmmm,vdw ) interactions to the MM potential, and V mm,pol is the many-body MM polarization energy.…”

“…Within LICHEM, the electron density is polarized by both the QM region and the static MM multipole moments [26]. A separate MM calculation is then performed to determine the response of the MM polarizable sites to the QM and MM electrostatic fields.…”

“…Within LICHEM, the scaled monopole, dipole, and quadrupole moments can be further approximated as a set of 6 point-charges in an octahedral arrangement [12, 19]. As was shown previously [26], the point-charge approximation is a simple and accurate method for including multipole moments in QM software that can only employ point-charges for the external field.…”

“…Separation of the optimizations: LICHEM employs the iterative QM/MM optimization algorithm [26, 52] shown in Fig. 4.…”