Next Article in Journal
Microbial Synthesis of Non-Natural Anthraquinone Glucosides Displaying Superior Antiproliferative Properties
Next Article in Special Issue
Exploring Peptide–Solvent Interactions: A Computational Study
Previous Article in Journal
GC-MS Study of the Chemical Components of Different Aquilaria sinensis (Lour.) Gilgorgans and Agarwood from Different Asian Countries
Previous Article in Special Issue
Improvement of Performance, Stability and Continuity by Modified Size-Consistent Multipartitioning Quantum Mechanical/Molecular Mechanical Method
Article Menu
Issue 9 (September) cover image

Export Article

Open AccessArticle
Molecules 2018, 23(9), 2170; https://doi.org/10.3390/molecules23092170

Adaptive QM/MM for Molecular Dynamics Simulations: 5. On the Energy-Conserved Permuted Adaptive-Partitioning Schemes

Department of Chemistry, University of Colorado Denver, Denver, CO 80217, USA
*
Author to whom correspondence should be addressed.
Received: 24 July 2018 / Revised: 23 August 2018 / Accepted: 24 August 2018 / Published: 28 August 2018
Full-Text   |   PDF [3319 KB, uploaded 29 August 2018]   |  

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. View Full-Text
Keywords: combined QM/MM; molecular dynamics simulations; energy conservation; radial distribution function; adaptive partitioning combined QM/MM; molecular dynamics simulations; energy conservation; radial distribution function; adaptive partitioning
Figures

Graphical abstract

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).
SciFeed

Share & Cite This Article

MDPI and ACS Style

Duster, A.W.; Wang, C.-H.; Lin, H. Adaptive QM/MM for Molecular Dynamics Simulations: 5. On the Energy-Conserved Permuted Adaptive-Partitioning Schemes. Molecules 2018, 23, 2170.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Molecules EISSN 1420-3049 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top