Validation of Molecular Simulation: An Overview of Issues

Wilfred F. van Gunsteren; Xavier Daura; Niels Hansen; Alan E. Mark; Chris Oostenbrink; Sereina Riniker; Lorna J. Smith

doi:10.1002/anie.201702945

Validation of Molecular Simulation: An Overview of Issues

Wilfred F. van Gunsteren, Xavier Daura, Niels Hansen, Alan E. Mark, Chris Oostenbrink, Sereina Riniker, Lorna J. Smith

Producció científica: Contribució a revista › Article de revisió › Recerca › Avaluat per experts

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KGaA, Weinheim. La simulació per ordinador de sistemes moleculars permet descriure relacions estructura-energia-funcionalitat de processos moleculars a nivell subatòmic, atòmic, supramatònic o supramolecular. Per interpretar correctament els resultats d'aquestes simulacions s'ha d'avaluar la qualitat de les propietats calculades. Això depèn de com es duen a terme les simulacions i de com es validen comparant-les amb valors Qexp de quantitats observables experimentalment, Q. S'ha de considerar 1) l'exactitud del Qexp, 2) l'exactitud de la funció Q(rN) utilitzada per calcular un valor Q basat en una configuració molecular rN de N partícules, 3) la sensibilitat de la funció Q(rN) a la configuració rN, 4) les escales temporals relatives de la simulació i l'experiment, 5) el grau d'equivalència entre propietats calculades i experimentals, i 6) el grau en què el sistema simulat coincideix amb les condicions experimentals. Les dades experimentals són limitades en abast i corresponen generalment a mitjanes tant temporals com espacials. Es presenta una anàlisi crítica dels diversos factors que influeixen l'aparent grau de (des)acord entre simulacions i experiments, il·lustrat per exemples extrets de la literatura. S'explica què es pot fer per millorar la validació de la simulació molecular. © 2018 Wiley-VCH Verlag GmbH

Idioma original	Anglès
Pàgines (de-a)	884-902
Revista	Angewandte Chemie - International Edition
Volum	57
Número	4
DOIs	https://doi.org/10.1002/anie.201702945
Estat de la publicació	Publicada - 22 de gen. 2018

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@article{86590fd825594e38957e4983cee22e39,

title = "Validation of Molecular Simulation: An Overview of Issues",

abstract = "{\textcopyright} 2018 Wiley-VCH Verlag GmbH \& Co. KGaA, Weinheim. Computer simulation of molecular systems enables structure–energy–function relationships of molecular processes to be described at the sub-atomic, atomic, supra-atomic, or supra-molecular level. To interpret results of such simulations appropriately, the quality of the calculated properties must be evaluated. This depends on the way the simulations are performed and on the way they are validated by comparison to values Qexp of experimentally observable quantities Q. One must consider 1) the accuracy of Qexp, 2) the accuracy of the function Q(rN) used to calculate a Q-value based on a molecular configuration rN of N particles, 3) the sensitivity of the function Q(rN) to the configuration rN, 4) the relative time scales of the simulation and experiment, 5) the degree to which the calculated and experimental properties are equivalent, and 6) the degree to which the system simulated matches the experimental conditions. Experimental data is limited in scope and generally corresponds to averages over both time and space. A critical analysis of the various factors influencing the apparent degree of (dis)agreement between simulations and experiment is presented and illustrated using examples from the literature. What can be done to enhance the validation of molecular simulation is also discussed.",

keywords = "computer chemistry, experimental data, molecular dynamics simulation, Monte Carlo simulation, pseudo-validation",

author = "\{van Gunsteren\}, \{Wilfred F.\} and Xavier Daura and Niels Hansen and Mark, \{Alan E.\} and Chris Oostenbrink and Sereina Riniker and Smith, \{Lorna J.\}",

year = "2018",

month = jan,

day = "22",

doi = "10.1002/anie.201702945",

language = "English",

volume = "57",

pages = "884--902",

journal = "Angewandte Chemie - International Edition",

issn = "1433-7851",

publisher = "John Wiley and Sons Inc.",

number = "4",

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TY - JOUR

T1 - Validation of Molecular Simulation: An Overview of Issues

AU - van Gunsteren, Wilfred F.

AU - Daura, Xavier

AU - Hansen, Niels

AU - Mark, Alan E.

AU - Oostenbrink, Chris

AU - Riniker, Sereina

AU - Smith, Lorna J.

PY - 2018/1/22

Y1 - 2018/1/22

N2 - © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim. Computer simulation of molecular systems enables structure–energy–function relationships of molecular processes to be described at the sub-atomic, atomic, supra-atomic, or supra-molecular level. To interpret results of such simulations appropriately, the quality of the calculated properties must be evaluated. This depends on the way the simulations are performed and on the way they are validated by comparison to values Qexp of experimentally observable quantities Q. One must consider 1) the accuracy of Qexp, 2) the accuracy of the function Q(rN) used to calculate a Q-value based on a molecular configuration rN of N particles, 3) the sensitivity of the function Q(rN) to the configuration rN, 4) the relative time scales of the simulation and experiment, 5) the degree to which the calculated and experimental properties are equivalent, and 6) the degree to which the system simulated matches the experimental conditions. Experimental data is limited in scope and generally corresponds to averages over both time and space. A critical analysis of the various factors influencing the apparent degree of (dis)agreement between simulations and experiment is presented and illustrated using examples from the literature. What can be done to enhance the validation of molecular simulation is also discussed.

AB - © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim. Computer simulation of molecular systems enables structure–energy–function relationships of molecular processes to be described at the sub-atomic, atomic, supra-atomic, or supra-molecular level. To interpret results of such simulations appropriately, the quality of the calculated properties must be evaluated. This depends on the way the simulations are performed and on the way they are validated by comparison to values Qexp of experimentally observable quantities Q. One must consider 1) the accuracy of Qexp, 2) the accuracy of the function Q(rN) used to calculate a Q-value based on a molecular configuration rN of N particles, 3) the sensitivity of the function Q(rN) to the configuration rN, 4) the relative time scales of the simulation and experiment, 5) the degree to which the calculated and experimental properties are equivalent, and 6) the degree to which the system simulated matches the experimental conditions. Experimental data is limited in scope and generally corresponds to averages over both time and space. A critical analysis of the various factors influencing the apparent degree of (dis)agreement between simulations and experiment is presented and illustrated using examples from the literature. What can be done to enhance the validation of molecular simulation is also discussed.

KW - computer chemistry

KW - experimental data

KW - molecular dynamics simulation

KW - Monte Carlo simulation

KW - pseudo-validation

UR - https://www.scopus.com/pages/publications/85038261886

U2 - 10.1002/anie.201702945

DO - 10.1002/anie.201702945

M3 - Review article

C2 - 28682472

SN - 1433-7851

VL - 57

SP - 884

EP - 902

JO - Angewandte Chemie - International Edition

JF - Angewandte Chemie - International Edition

IS - 4

ER -

Validation of Molecular Simulation: An Overview of Issues

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