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. 2024 May 7;160(17):174103.
doi: 10.1063/5.0200722.

Seamless integration of GEM, a density based-force field, for QM/MM simulations via LICHEM, Psi4, and Tinker-HP

Jorge Nochebuena  1 , Andrew C Simmonett  2 , G Andrés Cisneros  1   3
Affiliations

Seamless integration of GEM, a density based-force field, for QM/MM simulations via LICHEM, Psi4, and Tinker-HP

Jorge Nochebuena et al. J Chem Phys. .

Abstract

Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations have become an essential tool in computational chemistry, particularly for analyzing complex biological and condensed phase systems. Building on this foundation, our work presents a novel implementation of the Gaussian Electrostatic Model (GEM), a polarizable density-based force field, within the QM/MM framework. This advancement provides seamless integration, enabling efficient and optimized QM/GEM calculations in a single step using the LICHEM Code. We have successfully applied our implementation to water dimers and hexamers, demonstrating the ability to handle water systems with varying numbers of water molecules. Moreover, we have extended the application to describe the double proton transfer of the aspartic acid dimer in a box of water, which highlights the method's proficiency in investigating heterogeneous systems. Our implementation offers the flexibility to perform on-the-fly density fitting or to utilize pre-fitted coefficients to estimate exchange and Coulomb contributions. This flexibility enhances efficiency and accuracy in modeling molecular interactions, especially in systems where polarization effects are significant.

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Conflict of interest statement

The authors have no conflicts to disclose.

Figures

FIG. 1.
FIG. 1.
General process to calculate the QM/GEM* interaction energy using the LICHEM code.
FIG. 2.
FIG. 2.
(a)–(j) Smith water dimers.
FIG. 3.
FIG. 3.
AMOEBA water.
FIG. 4.
FIG. 4.
Hexamers. (a) Bag, (b) book1, (c) book2, (d) cage, (e) chair, and (f) prism.
FIG. 5.
FIG. 5.
Aspartic acid dimer in a water box. Red lines represent water molecules.
FIG. 6.
FIG. 6.
Interaction energies (left) and deviations (right) for the ten Smith water dimers. (a) and (b) show the two different options for the selection of the QM region. Mull and ESP represent Mulliken and electrostatic potential derived charges, respectively.
FIG. 7.
FIG. 7.
Violin plots comparing ωB97X-D//AMOEBA and ωB97X-D//GEM calculations for the different QM/MM combinations of the six water hexamers. The dashed horizontal lines in black, red, and green represent ωB97X-D-pure, AMOEBA-pure, and GEM-pure calculations, respectively.
FIG. 8.
FIG. 8.
Double proton transfer in a model aspartic acid dimer. (a)–(c) Reactant, transition state, and product structures, respectively. (d) Energy profile from the reaction coordinate.
See this image and copyright information in PMC

References

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