Abstract
Truncation is still chosen for many long-range intermolecular interaction calculations to efficiently compute free-boundary systems, macromolecular systems and net-charge molecular systems, for example. Advanced truncation methods have been developed for long-range intermolecular interactions. Every truncation method can be implemented as one of two basic cut-off schemes, namely either an atom-based or a group-based cut-off scheme. The former computes interactions of “atoms” inside the cut-off radius, whereas the latter computes interactions of “molecules” inside the cut-off radius. In this work, the effect of group-based cut-off is investigated for isotropic periodic sum (IPS) techniques, which are promising cut-off treatments to attain advanced accuracy for many types of molecular system. The effect of group-based cut-off is clearly different from that of atom-based cut-off, and severe artefacts are observed in some cases. However, no severe discrepancy from the Ewald sum is observed with the extended IPS techniques.
Highlights
Molecular dynamics (MD) simulations are expected to give new insights on a molecular level into complex systems, but they incur massive computational costs
linear-combination-based IPS (LIPS)-5th-group and LIPS-SW-group converge to particle mesh Ewald (PME) at cut-off radii longer than rc = 1.8 nm. These results show that LIPS-5th and LIPS-SW estimate the potential energy successfully despite using group-based cut-off
The liquid structure calculated by IPS method for non-polar systems (IPSn)-group had defects that were more serious than those calculated by IPSn-atom
Summary
Molecular dynamics (MD) simulations are expected to give new insights on a molecular level into complex systems, but they incur massive computational costs. The cause of this defect was investigated systematically, and a severe artefact around the cut-off distance was observed in the Kirkwood factor Gk(r)[28,30] This shows clearly that group-based cut-off causes serious artefacts in dipole–dipole correlations and stabilizes the anomalous layer structure in bulk water systems. This effect was observed for switch/shift functions and the reaction field method with group-based cut-off[28,30]. We carefully estimate the accuracy of IPS techniques with group-based cut-off for MD simulations of bulk water and water–vapour interfacial systems
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