دورية أكاديمية
Guidelines for Free-Energy Calculations Involving Charge Changes.
| العنوان: | Guidelines for Free-Energy Calculations Involving Charge Changes. |
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| المؤلفون: | Petrov D; Institute for Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering, University of Natural Resources and Life Sciences, Vienna, Vienna 1190, Austria., Perthold JW; Institute for Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering, University of Natural Resources and Life Sciences, Vienna, Vienna 1190, Austria., Oostenbrink C; Institute for Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering, University of Natural Resources and Life Sciences, Vienna, Vienna 1190, Austria.; Christian Doppler Laboratory for Molecular Informatics in the Biosciences, University of Natural Resources and Life Sciences, Vienna, Vienna 1190, Austria., de Groot BL; Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany., Gapsys V; Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany.; Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, Beerse B-2340, Belgium. |
| المصدر: | Journal of chemical theory and computation [J Chem Theory Comput] 2024 Jan 23; Vol. 20 (2), pp. 914-925. Date of Electronic Publication: 2024 Jan 02. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: American Chemical Society Country of Publication: United States NLM ID: 101232704 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1549-9626 (Electronic) Linking ISSN: 15499618 NLM ISO Abbreviation: J Chem Theory Comput Subsets: PubMed not MEDLINE; MEDLINE |
| أسماء مطبوعة: | Original Publication: Washington, D.C. : American Chemical Society, c2005- |
| مستخلص: | The Coulomb interactions in molecular simulations are inherently approximated due to the finite size of the molecular box sizes amenable to current-day compute power. Several methods exist for treating long-range electrostatic interactions, yet these approaches are subject to various finite-size-related artifacts. Lattice-sum methods are frequently used to approximate long-range interactions; however, these approaches also suffer from artifacts which become particularly pronounced for free-energy calculations that involve charge changes. The artifacts, however, also affect the sampling when plain simulations are performed, leading to a biased ensemble. Here, we investigate two previously described model systems to determine if artifacts continue to play a role when overall neutral boxes are considered, in the context of both free-energy calculations and sampling. We find that ensuring that no net-charge changes take place, while maintaining a neutral simulation box, may be sufficient provided that the simulation boxes are large enough. Addition of salt to the solution (when appropriate) can further alleviate the remaining artifacts in the sampling or the calculated free-energy differences. We provide practical guidelines to avoid finite-size artifacts. |
| References: | J Phys Chem A. 2017 Feb 23;121(7):1525-1530. (PMID: 28152306) J Comput Aided Mol Des. 2015 May;29(5):397-411. (PMID: 25808134) J Chem Theory Comput. 2014 Jan 14;10(1):381-90. (PMID: 26579917) Elife. 2019 Jun 20;8:. (PMID: 31219782) J Chem Theory Comput. 2014 Jul 8;10(7):2690-709. (PMID: 26586504) J Chem Theory Comput. 2020 Dec 8;16(12):7721-7734. (PMID: 33136389) J Comput Chem. 2014 Jan 30;35(3):227-43. (PMID: 24249099) Theor Chem Acc. 2015;134(2):2. (PMID: 26097404) J Chem Phys. 2011 Apr 14;134(14):144104. (PMID: 21495739) J Chem Phys. 2006 Mar 28;124(12):124106. (PMID: 16599661) Biophys J. 2013 Jan 8;104(1):196-207. (PMID: 23332072) J Comput Chem. 2015 Feb 15;36(5):348-54. (PMID: 25487359) Eur Biophys J. 2011 Jul;40(7):843-56. (PMID: 21533652) Elife. 2020 Aug 19;9:. (PMID: 32812868) J Chem Phys. 2006 Jun 14;124(22):224501. (PMID: 16784292) J Phys Chem B. 2022 Sep 15;126(36):6868-6877. (PMID: 36049129) J Chem Phys. 2008 Sep 28;129(12):124105. (PMID: 19045004) J Comput Chem. 2009 Jan 30;30(2):212-21. (PMID: 18785242) Methods Mol Biol. 2015;1215:173-209. (PMID: 25330964) J Chem Theory Comput. 2018 Dec 11;14(12):6346-6358. (PMID: 30375870) J Chem Phys. 2007 Jan 7;126(1):014101. (PMID: 17212484) |
| تواريخ الأحداث: | Date Created: 20240102 Latest Revision: 20240127 |
| رمز التحديث: | 20240127 |
| مُعرف محوري في PubMed: | PMC10809403 |
| DOI: | 10.1021/acs.jctc.3c00757 |
| PMID: | 38164763 |
| قاعدة البيانات: | MEDLINE |
Find this issue from the American Chemical Society | تدمد: | 1549-9626 |
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| DOI: | 10.1021/acs.jctc.3c00757 |