Year-end Sale % OFF 
Abstract
The implementation and validation of the adaptive buffered force (AdBF) quantum-mechanics/molecular-mechanics (QM/MM) method in two popular packages, CP2K and AMBER are presented. The implementations build on the existing QM/MM functionality in each code, extending it to allow for redefinition of the QM and MM regions during the simulation and reducing QM-MM interface errors by discarding forces near the boundary according to the buffered force-mixing approach. New adaptive thermostats, needed by force-mixing methods, are also implemented. Different variants of the method are benchmarked by simulating the structure of bulk water, water autoprotolysis in the presence of zinc and dimethyl-phosphate hydrolysis using various semiempirical Hamiltonians and density functional theory as the QM model. It is shown that with suitable parameters, based on force convergence tests, the AdBF QM/MM scheme can provide an accurate approximation of the structure in the dynamical QM region matching the corresponding fully QM simulations, as well as reproducing the correct energetics in all cases. Adaptive unbuffered force-mixing and adaptive conventional QM/MM methods also provide reasonable results for some systems, but are more likely to suffer from instabilities and inaccuracies. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
Highlights
Quantum-mechanics/molecular-mechanics (QM/MM) methods[1] have matured over the past few decades and are an essential tool for modeling chemical reactions of complex systems
The radius of the QM region models rbuffer in the adbf-QM/MM method’s extended QM calculation, since it controls the distance between the molecule whose forces we are testing and the QM-MM interface
The QM/MM approach has been widely used for simulating processes that require a quantummechanical description in a small region, for example a reaction with covalent bond rearrangement, within a larger system with important long-range structure, such as a protein or a polar solvent
Summary
Quantum-mechanics/molecular-mechanics (QM/MM) methods[1] have matured over the past few decades and are an essential tool for modeling chemical reactions of complex systems. The QM and MM subsystems affect each other directly, by covalent, electrostatic, or other non-bonded interactions, as well as implicitly through long-range structure in the MM subsystem Capturing such long range interactions can be essential even for the description of the local structure, e.g. a in protein where the reaction involves residues that are kept in place by the structure of the rest of the protein, or because long range electrostatic effects play a direct role in the reaction.[2,3]. The accuracy of the conventional approach depends on the appropriateness of using a fixed set of atoms in the QM region, and on the ability of the QM-MM interaction term to eliminate the fictitious boundary effects in the QM and MM subsystem calculations
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
