FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W1974369408> ?p ?o ?g. }

• W1974369408 endingPage "5735" @default.
• W1974369408 startingPage "5728" @default.
• W1974369408 abstract "Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations provide a powerful tool for studying chemical reactions, especially in complex biochemical systems. In most works to date, the quantum region is kept fixed throughout the simulation and is defined in an ad hoc way based on chemical intuition and available computational resources. The simulation errors associated with a given choice of the quantum region are, however, rarely assessed in a systematic manner. Here we study the dependence of two relevant quantities on the QM region size: the force error at the center of the QM region and the free energy of a proton transfer reaction. Taking lysozyme as our model system, we find that in an apolar region the average force error rapidly decreases with increasing QM region size. In contrast, the average force error at the polar active site is considerably higher, exhibits large oscillations and decreases more slowly, and may not fall below acceptable limits even for a quantum region radius of 9.0 A. Although computation of free energies could only be afforded until 6.0 A, results were found to change considerably within these limits. These errors demonstrate that the results of QM/MM calculations are heavily affected by the definition of the QM region (not only its size), and a convergence test is proposed to be a part of setting up QM/MM simulations." @default.
• W1974369408 created "2016-06-24" @default.
• W1974369408 creator A5013000080 @default.
• W1974369408 creator A5025442671 @default.
• W1974369408 creator A5045294791 @default.
• W1974369408 creator A5052058110 @default.
• W1974369408 creator A5062555137 @default.
• W1974369408 creator A5077728085 @default.
• W1974369408 creator A5078144452 @default.
• W1974369408 date "2009-04-02" @default.
• W1974369408 modified "2023-10-17" @default.
• W1974369408 title "Evaluating Boundary Dependent Errors in QM/MM Simulations" @default.
• W1974369408 cites W1967165000 @default.
• W1974369408 cites W1975364540 @default.
• W1974369408 cites W1976499671 @default.
• W1974369408 cites W1986025575 @default.
• W1974369408 cites W1994360824 @default.
• W1974369408 cites W2001834673 @default.
• W1974369408 cites W2004303971 @default.
• W1974369408 cites W2014574246 @default.
• W1974369408 cites W2015707881 @default.
• W1974369408 cites W2022950330 @default.
• W1974369408 cites W2024872256 @default.
• W1974369408 cites W2026054984 @default.
• W1974369408 cites W2027815611 @default.
• W1974369408 cites W2029186981 @default.
• W1974369408 cites W2031314489 @default.
• W1974369408 cites W2035751951 @default.
• W1974369408 cites W2038417675 @default.
• W1974369408 cites W2057052341 @default.
• W1974369408 cites W2082265166 @default.
• W1974369408 cites W2086786922 @default.
• W1974369408 cites W2094941054 @default.
• W1974369408 cites W2103125723 @default.
• W1974369408 cites W2107031937 @default.
• W1974369408 cites W2115718697 @default.
• W1974369408 cites W2122199548 @default.
• W1974369408 cites W2127336290 @default.
• W1974369408 cites W2134497066 @default.
• W1974369408 cites W2136913776 @default.
• W1974369408 cites W2140884041 @default.
• W1974369408 cites W2149507711 @default.
• W1974369408 cites W2154181301 @default.
• W1974369408 cites W2171893485 @default.
• W1974369408 cites W3102225598 @default.
• W1974369408 cites W4293570254 @default.
• W1974369408 doi "https://doi.org/10.1021/jp807277r" @default.
• W1974369408 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/19341253" @default.
• W1974369408 hasPublicationYear "2009" @default.
• W1974369408 type Work @default.
• W1974369408 sameAs 1974369408 @default.
• W1974369408 citedByCount "54" @default.
• W1974369408 countsByYear W19743694082012 @default.
• W1974369408 countsByYear W19743694082013 @default.
• W1974369408 countsByYear W19743694082014 @default.
• W1974369408 countsByYear W19743694082015 @default.
• W1974369408 countsByYear W19743694082016 @default.
• W1974369408 countsByYear W19743694082017 @default.
• W1974369408 countsByYear W19743694082018 @default.
• W1974369408 countsByYear W19743694082019 @default.
• W1974369408 countsByYear W19743694082020 @default.
• W1974369408 countsByYear W19743694082021 @default.
• W1974369408 countsByYear W19743694082022 @default.
• W1974369408 countsByYear W19743694082023 @default.
• W1974369408 crossrefType "journal-article" @default.
• W1974369408 hasAuthorship W1974369408A5013000080 @default.
• W1974369408 hasAuthorship W1974369408A5025442671 @default.
• W1974369408 hasAuthorship W1974369408A5045294791 @default.
• W1974369408 hasAuthorship W1974369408A5052058110 @default.
• W1974369408 hasAuthorship W1974369408A5062555137 @default.
• W1974369408 hasAuthorship W1974369408A5077728085 @default.
• W1974369408 hasAuthorship W1974369408A5078144452 @default.
• W1974369408 hasConcept C111472728 @default.
• W1974369408 hasConcept C11413529 @default.
• W1974369408 hasConcept C121332964 @default.
• W1974369408 hasConcept C121864883 @default.
• W1974369408 hasConcept C132010649 @default.
• W1974369408 hasConcept C138885662 @default.
• W1974369408 hasConcept C20803032 @default.
• W1974369408 hasConcept C33923547 @default.
• W1974369408 hasConcept C45374587 @default.
• W1974369408 hasConcept C59593255 @default.
• W1974369408 hasConcept C62520636 @default.
• W1974369408 hasConcept C84114770 @default.
• W1974369408 hasConceptScore W1974369408C111472728 @default.
• W1974369408 hasConceptScore W1974369408C11413529 @default.
• W1974369408 hasConceptScore W1974369408C121332964 @default.
• W1974369408 hasConceptScore W1974369408C121864883 @default.
• W1974369408 hasConceptScore W1974369408C132010649 @default.
• W1974369408 hasConceptScore W1974369408C138885662 @default.
• W1974369408 hasConceptScore W1974369408C20803032 @default.
• W1974369408 hasConceptScore W1974369408C33923547 @default.
• W1974369408 hasConceptScore W1974369408C45374587 @default.
• W1974369408 hasConceptScore W1974369408C59593255 @default.
• W1974369408 hasConceptScore W1974369408C62520636 @default.
• W1974369408 hasConceptScore W1974369408C84114770 @default.
• W1974369408 hasIssue "17" @default.
• W1974369408 hasLocation W19743694081 @default.

• next