Cite this publication
Optimization and benchmarking of a perturbative Metropolis Monte Carlo quantum mechanics/molecular mechanics program
Feldt, J.; Miranda, S.; Pratas, F.; Roma, N.; Tomás, P. & Mata, R. A. (2017)
The Journal of Chemical Physics, 147(24) art. 244105. DOI: https://doi.org/10.1063/1.5009820
Documents & Media
- Feldt, Jonas; Miranda, Sebastião; Pratas, Frederico; Roma, Nuno; Tomás, Pedro; Mata, Ricardo A.
- In this work, we present an optimized perturbative quantum mechanics/molecular mechanics (QM/MM) method for use in Metropolis Monte Carlo simulations. The model adopted is particularly tailored for the simulation of molecular systems in solution but can be readily extended to other applications, such as catalysis in enzymatic environments. The electrostatic coupling between the QM and MM systems is simplified by applying perturbation theory to estimate the energy changes caused by a movement in the MM system. This approximation, together with the effective use of GPU acceleration, leads to a negligible added computational cost for the sampling of the environment. Benchmark calculations are carried out to evaluate the impact of the approximations applied and the overall computational performance.
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- The Journal of Chemical Physics
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