FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W2764109108> ?p ?o ?g. }

• W2764109108 endingPage "5752" @default.
• W2764109108 startingPage "5745" @default.
• W2764109108 abstract "Combined quantum mechanical and molecular mechanical (QM/MM) calculations is a popular approach to study enzymatic reactions. They are often based on a set of minimized structures obtained on snapshots from a molecular dynamics simulation to include some dynamics of the enzyme. It has been much discussed how the individual energies should be combined to obtain a final estimate of the energy, but the current consensus seems to be to use an exponential average. Then, the question is how many snapshots are needed to reach a reliable estimate of the energy. In this paper, I show that the question can be easily be answered if it is assumed that the energies follow a Gaussian distribution. Then, the outcome can be simulated based on a single parameter, σ, the standard deviation of the QM/MM energies from the various snapshots, and the number of required snapshots can be estimated once the desired accuracy and confidence of the result has been specified. Results for various parameters are presented, and it is shown that many more snapshots are required than is normally assumed. The number can be reduced by employing a cumulant approximation to second order. It is shown that most convergence criteria work poorly, owing to the very bad conditioning of the exponential average when σ is large (more than ∼7 kJ/mol), because the energies that contribute most to the exponential average have a very low probability. On the other hand, σ serves as an excellent convergence criterion." @default.
• W2764109108 created "2017-10-20" @default.
• W2764109108 creator A5030625494 @default.
• W2764109108 date "2017-10-26" @default.
• W2764109108 modified "2023-10-18" @default.
• W2764109108 title "How Many Conformations Need To Be Sampled To Obtain Converged QM/MM Energies? The Curse of Exponential Averaging" @default.
• W2764109108 cites W1904813316 @default.
• W2764109108 cites W1963938346 @default.
• W2764109108 cites W1965612527 @default.
• W2764109108 cites W1971290752 @default.
• W2764109108 cites W1972324757 @default.
• W2764109108 cites W1973448259 @default.
• W2764109108 cites W1987147145 @default.
• W2764109108 cites W1989195611 @default.
• W2764109108 cites W1989715615 @default.
• W2764109108 cites W1989958293 @default.
• W2764109108 cites W1998365857 @default.
• W2764109108 cites W1999925182 @default.
• W2764109108 cites W2000101045 @default.
• W2764109108 cites W2006228399 @default.
• W2764109108 cites W2012041836 @default.
• W2764109108 cites W2027279463 @default.
• W2764109108 cites W2027684389 @default.
• W2764109108 cites W2041775215 @default.
• W2764109108 cites W2053079455 @default.
• W2764109108 cites W2054173664 @default.
• W2764109108 cites W2059832777 @default.
• W2764109108 cites W2064002418 @default.
• W2764109108 cites W2071963550 @default.
• W2764109108 cites W2076017392 @default.
• W2764109108 cites W2079459513 @default.
• W2764109108 cites W2084961110 @default.
• W2764109108 cites W2110872379 @default.
• W2764109108 cites W2132645493 @default.
• W2764109108 cites W2134304763 @default.
• W2764109108 cites W2233659849 @default.
• W2764109108 cites W2315914087 @default.
• W2764109108 cites W2317054679 @default.
• W2764109108 cites W2317961599 @default.
• W2764109108 cites W2321511863 @default.
• W2764109108 cites W2333133041 @default.
• W2764109108 cites W2335804930 @default.
• W2764109108 cites W2344666683 @default.
• W2764109108 cites W2484443252 @default.
• W2764109108 cites W2499316751 @default.
• W2764109108 cites W2562368273 @default.
• W2764109108 cites W2564465552 @default.
• W2764109108 cites W2599323046 @default.
• W2764109108 cites W2759770439 @default.
• W2764109108 cites W4211198032 @default.
• W2764109108 doi "https://doi.org/10.1021/acs.jctc.7b00826" @default.
• W2764109108 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/29024586" @default.
• W2764109108 hasPublicationYear "2017" @default.
• W2764109108 type Work @default.
• W2764109108 sameAs 2764109108 @default.
• W2764109108 citedByCount "64" @default.
• W2764109108 countsByYear W27641091082018 @default.
• W2764109108 countsByYear W27641091082019 @default.
• W2764109108 countsByYear W27641091082020 @default.
• W2764109108 countsByYear W27641091082021 @default.
• W2764109108 countsByYear W27641091082022 @default.
• W2764109108 countsByYear W27641091082023 @default.
• W2764109108 crossrefType "journal-article" @default.
• W2764109108 hasAuthorship W2764109108A5030625494 @default.
• W2764109108 hasBestOaLocation W27641091082 @default.
• W2764109108 hasConcept C121332964 @default.
• W2764109108 hasConcept C121864883 @default.
• W2764109108 hasConcept C134306372 @default.
• W2764109108 hasConcept C151376022 @default.
• W2764109108 hasConcept C162324750 @default.
• W2764109108 hasConcept C163716315 @default.
• W2764109108 hasConcept C18762648 @default.
• W2764109108 hasConcept C2777303404 @default.
• W2764109108 hasConcept C28826006 @default.
• W2764109108 hasConcept C33923547 @default.
• W2764109108 hasConcept C41008148 @default.
• W2764109108 hasConcept C50522688 @default.
• W2764109108 hasConcept C59593255 @default.
• W2764109108 hasConcept C62520636 @default.
• W2764109108 hasConcept C84114770 @default.
• W2764109108 hasConceptScore W2764109108C121332964 @default.
• W2764109108 hasConceptScore W2764109108C121864883 @default.
• W2764109108 hasConceptScore W2764109108C134306372 @default.
• W2764109108 hasConceptScore W2764109108C151376022 @default.
• W2764109108 hasConceptScore W2764109108C162324750 @default.
• W2764109108 hasConceptScore W2764109108C163716315 @default.
• W2764109108 hasConceptScore W2764109108C18762648 @default.
• W2764109108 hasConceptScore W2764109108C2777303404 @default.
• W2764109108 hasConceptScore W2764109108C28826006 @default.
• W2764109108 hasConceptScore W2764109108C33923547 @default.
• W2764109108 hasConceptScore W2764109108C41008148 @default.
• W2764109108 hasConceptScore W2764109108C50522688 @default.
• W2764109108 hasConceptScore W2764109108C59593255 @default.
• W2764109108 hasConceptScore W2764109108C62520636 @default.
• W2764109108 hasConceptScore W2764109108C84114770 @default.
• W2764109108 hasFunder F4320320366 @default.
• W2764109108 hasFunder F4320322327 @default.
• W2764109108 hasFunder F4320322581 @default.

• next