Abstract
In combined quantum-mechanical/molecular-mechanical (QM/MM) dynamics simulations, the adaptive-partitioning (AP) schemes reclassify atoms on-the-fly as QM or MM in a smooth manner. This yields a mobile QM subsystem with contents that are continuously updated as needed. Here, we tailor the Hamiltonian adaptive many-body correction (HAMBC) proposed by Boreboom et al. [J. Chem. Theory Comput. 2016, 12, 3441] to the permuted AP (PAP) scheme. The treatments lead to the HAMBC-PAP method (HPAP), which both conserves energy and produces accurate solvation structures in the test of “water-in-water” model system.
Highlights
A challenge in permuted adaptive partitioning (PAP) concerns the gradients gradients due to the smoothing functions employed in the interpolation procedure, which, if not due to the smoothing functions employed in the interpolation procedure, which, if not negligible, negligible, may cause artefacts in the Molecular dynamics (MD) simulations [30,35,42,46]
If the modified PAP (mPAP) potential is truncated at a low order p and if N p, which is the case in our ( p) current simulations, the average is dominated by the p-th order ∆Ei, which has the largest number of partitions: ( p) h∆Ei i ≈ h∆Ei i
We examined the solvation structure around the solute water by computing the pairwise radial distribution function (RDF) gO’O (r) between its oxygen (O′, serving as the center of the active zone) distribution function (RDF) gO’O (r ) between its oxygen (O0, serving as the center of the active zone) and the surrounding oxygen (O) atoms for the original PAP, mPAP, and HAMBC-PAP method (HPAP) simulations under and the surrounding oxygen (O) atoms for the original PAP, mPAP, and HPAP simulations under constant temperature (Figure 5a)
Summary
Molecular dynamics (MD) simulations of diffusive systems, such as the diffusion of a solute (a solvated ion or molecule) through solvent, has been a challenging task for multiscale methods, especially for combined quantum-mechanics/molecular-mechanics (QM/MM) methods [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26]. A challenge in PAP (and other distance-based adaptive QM/MM methods) concerns the gradients gradients due to the smoothing functions employed in the interpolation procedure, which, if not due to the smoothing functions employed in the interpolation procedure, which, if not negligible, negligible, may cause artefacts in the MD simulations [30,35,42,46] These forces, which are sometimes may cause artefacts in the MD simulations [30,35,42,46]. Inspired by the works of the molecular-mechanics/course-grained (MM/CG) community, especially the Hamiltonian adaptive resolution scheme (H-AdResS) by Potestio et al [53] the HAMBC method includes per-molecule-based correction terms to the SAP QM/MM Hamiltonian. We demonstrate that the correction can be taken as a function of the value of the smoothing function even when the PAP potential is truncated
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