Efficient minimization of multipole electrostatic potentials in torsion space
The development of models of macromolecular electrostatics capable of delivering improved fidelity to quantum mechanical calculations is an active field of research in computational chemistry. Most molecular force field development takes place in the context of models with full Cartesian coordinate...
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description | The development of models of macromolecular electrostatics capable of delivering improved fidelity to quantum mechanical calculations is an active field of research in computational chemistry. Most molecular force field development takes place in the context of models with full Cartesian coordinate degrees of freedom. Nevertheless, a number of macromolecular modeling programs use a reduced set of conformational variables limited to rotatable bonds. Efficient algorithms for minimizing the energies of macromolecular systems with torsional degrees of freedom have been developed with the assumption that all atom-atom interaction potentials are isotropic. We describe novel modifications to address the anisotropy of higher order multipole terms while retaining the efficiency of these approaches. In addition, we present a treatment for obtaining derivatives of atom-centered tensors with respect to torsional degrees of freedom. We apply these results to enable minimization of the Amoeba multipole electrostatics potential in a system with torsional degrees of freedom, and validate the correctness of the gradients by comparison to finite difference approximations. In the interest of enabling a complete model of electrostatics with implicit treatment of solvent-mediated effects, we also derive expressions for the derivative of solvent accessible surface area with respect to torsional degrees of freedom. |
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Most molecular force field development takes place in the context of models with full Cartesian coordinate degrees of freedom. Nevertheless, a number of macromolecular modeling programs use a reduced set of conformational variables limited to rotatable bonds. Efficient algorithms for minimizing the energies of macromolecular systems with torsional degrees of freedom have been developed with the assumption that all atom-atom interaction potentials are isotropic. We describe novel modifications to address the anisotropy of higher order multipole terms while retaining the efficiency of these approaches. In addition, we present a treatment for obtaining derivatives of atom-centered tensors with respect to torsional degrees of freedom. We apply these results to enable minimization of the Amoeba multipole electrostatics potential in a system with torsional degrees of freedom, and validate the correctness of the gradients by comparison to finite difference approximations. In the interest of enabling a complete model of electrostatics with implicit treatment of solvent-mediated effects, we also derive expressions for the derivative of solvent accessible surface area with respect to torsional degrees of freedom.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0195578</identifier><identifier>PMID: 29641557</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Algorithms ; Amoeba ; Analysis ; Anisotropy ; Biochemistry ; Biology and Life Sciences ; Biophysics ; Chemical bonds ; Computational chemistry ; Computer applications ; Degrees of freedom ; Electric potential ; Electrostatic properties ; Electrostatics ; Macromolecules ; Models, Molecular ; Molecular Conformation ; Molecular modelling ; Optimization ; Physical Sciences ; Proteins ; Quantum mechanics ; Quantum Theory ; Rotation ; Solvents ; Solvents - chemistry ; Static Electricity ; Surface area ; Surface Properties ; Tensors ; Thermodynamics ; Torsion</subject><ispartof>PloS one, 2018-04, Vol.13 (4), p.e0195578-e0195578</ispartof><rights>COPYRIGHT 2018 Public Library of Science</rights><rights>2018 Bodmer, Havranek. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2018 Bodmer, Havranek 2018 Bodmer, Havranek</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c641t-d8f9ced4e28bb7bddeba0941449b743a8fc3e5802f12ed4eb6bc7aef10dca5e3</cites><orcidid>0000-0001-8241-5928</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5895050/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5895050/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2100,2919,23857,27915,27916,53782,53784,79361,79362</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29641557$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Salsbury, Freddie</contributor><creatorcontrib>Bodmer, Nicholas K</creatorcontrib><creatorcontrib>Havranek, James J</creatorcontrib><title>Efficient minimization of multipole electrostatic potentials in torsion space</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The development of models of macromolecular electrostatics capable of delivering improved fidelity to quantum mechanical calculations is an active field of research in computational chemistry. Most molecular force field development takes place in the context of models with full Cartesian coordinate degrees of freedom. Nevertheless, a number of macromolecular modeling programs use a reduced set of conformational variables limited to rotatable bonds. Efficient algorithms for minimizing the energies of macromolecular systems with torsional degrees of freedom have been developed with the assumption that all atom-atom interaction potentials are isotropic. We describe novel modifications to address the anisotropy of higher order multipole terms while retaining the efficiency of these approaches. In addition, we present a treatment for obtaining derivatives of atom-centered tensors with respect to torsional degrees of freedom. We apply these results to enable minimization of the Amoeba multipole electrostatics potential in a system with torsional degrees of freedom, and validate the correctness of the gradients by comparison to finite difference approximations. 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Most molecular force field development takes place in the context of models with full Cartesian coordinate degrees of freedom. Nevertheless, a number of macromolecular modeling programs use a reduced set of conformational variables limited to rotatable bonds. Efficient algorithms for minimizing the energies of macromolecular systems with torsional degrees of freedom have been developed with the assumption that all atom-atom interaction potentials are isotropic. We describe novel modifications to address the anisotropy of higher order multipole terms while retaining the efficiency of these approaches. In addition, we present a treatment for obtaining derivatives of atom-centered tensors with respect to torsional degrees of freedom. We apply these results to enable minimization of the Amoeba multipole electrostatics potential in a system with torsional degrees of freedom, and validate the correctness of the gradients by comparison to finite difference approximations. 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subjects | Algorithms Amoeba Analysis Anisotropy Biochemistry Biology and Life Sciences Biophysics Chemical bonds Computational chemistry Computer applications Degrees of freedom Electric potential Electrostatic properties Electrostatics Macromolecules Models, Molecular Molecular Conformation Molecular modelling Optimization Physical Sciences Proteins Quantum mechanics Quantum Theory Rotation Solvents Solvents - chemistry Static Electricity Surface area Surface Properties Tensors Thermodynamics Torsion |
title | Efficient minimization of multipole electrostatic potentials in torsion space |
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