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An Efficient Linear-Scaling Electrostatic Coupling for Treating Periodic Boundary Conditions in QM/MM Simulations
Abstract
A new linear-scaling method based on a multigrid approach to treat long-range electrostatic interactions in hybrid quantum mechanics/molecular mechanics (QM/MM) simulations is described. The scheme has been implemented in the context of a QM calculation based on density functional theory (DFT). The method is tested on an analytical model to validate the new algorithm. Two realistic problems in α-quartz crystals and a zwitterionic dipeptide (GLY-ALA) in water have been chosen as further tests. Results from QM/MM calculations with periodic boundary conditions (PBC) show that the use of PBC is essential when studying highly ordered crystal structures, unless a carefully designed MM crystal is used for the calculation. With a general shaped MM subsystem, the absence of PBC leads to an incorrect description of Kohn-Sham band gaps and charge density. The present method allows periodic boundary conditions to be used in molecular simulations of biological and material science systems.
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Cited by
Kühne, T. D., Iannuzzi, M., Del Ben, M., Rybkin, V. V., Seewald, P., Stein, F., Laino, T., Khaliullin, R. Z., Schütt, O., Schiffmann, F., et al. (2020) · The Journal of Chemical Physics · doi:10.1063/5.0007045 · Cited by 4,468
Self-citationQM/MM Methods for Biological Systems
Senn, H. M., & Thiel, W. (2006) · Topics in Current Chemistry · doi:10.1007/128_2006_084 · Cited by 428
Senn, H. M., & Thiel, W. (2007) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2007.01.684 · Cited by 375
Classical Electrostatics for Biomolecular Simulations
Cisneros, G. A., Karttunen, M., Ren, P., & Sagui, C. (2014) · Chemical Reviews · doi:10.1021/cr300461d · Cited by 259
Metadata
- Authors
- Laino, T., Mohamed, F., Laio, A., & Parrinello, M.
- Venue
- Journal of Chemical Theory and Computation
- Publisher
- American Chemical Society (ACS)
- Published
- 2006-08-05
- Volume
- 2
- Issue
- 5
- Pages
- 1370-1378
- ISSN
- 1549-9618 (ISSN-L)
- 1549-9626
- OpenAlex
- W2089799306
- Cited by
- 171
- References
- 0
- FWCI
- 2.58
- Type
- journal article
- Language
- en
- Open access
- closed
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- Laino, T., Mohamed, F., Laio, A., & Parrinello, M. (2006). An Efficient Linear-Scaling Electrostatic Coupling for Treating Periodic Boundary Conditions in QM/MM Simulations. Journal of Chemical Theory and Computation. https://doi.org/10.1021/ct6001169
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