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A quantum chemical treatment of solvation effects using the standard quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations is challenging due to QM and MM solvent exchange near the QM solute. To this end, various adaptive QM/MM methods have been proposed, free solvent exchanges are allowed via flexible switching of their identities between QM and MM systems depending on their distances from the QM solute. However, temporal and spatial discontinuities remain in the standard implementations of adaptive QM/MM approaches and continue to hamper stable and accurate dynamics simulations. We previously demonstrated that the size-consistent multi-partitioning (SCMP) method achieves temporal continuity while, to some extent, avoiding spatial discontinuities. In the present study, we demonstrate that residual spatial discontinuities may lead to severe artifacts under certain conditions. Through quantitative analyses, we show that all multiscale including QM/MM methods might experience these problems, which, so far, have not been investigated in depth. To alleviate these artifacts, we propose a correction scheme in the framework of the SCMP approach and demonstrate its effectiveness using bulk water simulations.
This article was published in the following journal.
Name: Journal of chemical theory and computation
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Locations, on the GENOME, of GENES or other genetic elements that encode or control the expression of a quantitative trait (QUANTITATIVE TRAIT, HERITABLE).
Works consisting of studies using a quantitative method of combining the results of independent studies (usually drawn from the published literature) and synthesizing summaries and conclusions which may be used to evaluate therapeutic effectiveness, plan new studies, etc. It is often an overview of clinical trials. It is usually called a meta-analysis by the author or sponsoring body and should be differentiated from reviews of literature.
The application of STATISTICS to biological systems and organisms involving the retrieval or collection, analysis, reduction, and interpretation of qualitative and quantitative data.
Any visible result of a procedure which is caused by the procedure itself and not by the entity being analyzed. Common examples include histological structures introduced by tissue processing, radiographic images of structures that are not naturally present in living tissue, and products of chemical reactions that occur during analysis.
Works about clinical studies in which a prospectively planned opportunity is included to modify trial designs and hypotheses based on analysis of data from subjects in the study .