Development of Coarse‐Grained Force Field by Combining Multilinear Interpolation Technique and Simplex Algorithm
A fast, reasonable, and transferable coarse‐grained (CG) molecular dynamics force field (FF) is essential to combine experimental and simulation data. However, the parameterization of CG FF usually requires massive computation, which hinders its rapid development. Here, we presented an efficient opt...
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creator | Wan, Mingwei Song, Junjie Li, Wenli Gao, Lianghui Fang, Weihai |
description | A fast, reasonable, and transferable coarse‐grained (CG) molecular dynamics force field (FF) is essential to combine experimental and simulation data. However, the parameterization of CG FF usually requires massive computation, which hinders its rapid development. Here, we presented an efficient optimization protocol by combining multilinear interpolation technique with simplex algorithm. In this preliminary work, taking the experimental properties as the benchmark, we constructed a new set of CG FF for water and n‐alkanes by adopting piecewise Morse function to describe the nonbonded interactions. This CG FF has a delicate balance between efficiency, accuracy, and transferability and well reproduced the correct structural and thermodynamics properties of pure water and alkane liquids. More importantly, optimized Morse potential was also successfully applied to describe the interactions between water and n‐alkanes. It nicely predicted the phase separation, interface tension, hydration free energy, and formation of microemulsions of water/oil mixtures. © 2019 Wiley Periodicals, Inc.
The combination of global search and local refinement is essential in complex force field development. Here, the authors presented a global multilinear interpolation method (MIP) that is fast and easy to be implemented. As a demo, the authors combined MIP with a local simplex algorithm to develop efficient, accurate, and transferrable coarse‐grained force fields for water and alkanes. Routine of MIP combined with simplex. |
doi_str_mv | 10.1002/jcc.26131 |
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The combination of global search and local refinement is essential in complex force field development. Here, the authors presented a global multilinear interpolation method (MIP) that is fast and easy to be implemented. As a demo, the authors combined MIP with a local simplex algorithm to develop efficient, accurate, and transferrable coarse‐grained force fields for water and alkanes. Routine of MIP combined with simplex.</description><identifier>ISSN: 0192-8651</identifier><identifier>EISSN: 1096-987X</identifier><identifier>DOI: 10.1002/jcc.26131</identifier><identifier>PMID: 31859392</identifier><language>eng</language><publisher>Hoboken, USA: John Wiley & Sons, Inc</publisher><subject>Algorithms ; Alkanes ; Coarsening ; coarse‐grained force field ; Computer simulation ; Free energy ; hydrocarbon ; Interpolation ; Microemulsions ; Molecular dynamics ; Morse potential ; multilinear interpolation ; Optimization ; Parameterization ; Phase separation ; simplex ; Surface tension ; water</subject><ispartof>Journal of computational chemistry, 2020-03, Vol.41 (8), p.814-829</ispartof><rights>2019 Wiley Periodicals, Inc.</rights><rights>2020 Wiley Periodicals, Inc.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3531-1337980783a5cbdfd396a57ee16c4acd16cb424fde3310b34c8835df197bc2443</citedby><cites>FETCH-LOGICAL-c3531-1337980783a5cbdfd396a57ee16c4acd16cb424fde3310b34c8835df197bc2443</cites><orcidid>0000-0003-4414-3671 ; 0000-0002-1668-465X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fjcc.26131$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fjcc.26131$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1417,27924,27925,45574,45575</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31859392$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wan, Mingwei</creatorcontrib><creatorcontrib>Song, Junjie</creatorcontrib><creatorcontrib>Li, Wenli</creatorcontrib><creatorcontrib>Gao, Lianghui</creatorcontrib><creatorcontrib>Fang, Weihai</creatorcontrib><title>Development of Coarse‐Grained Force Field by Combining Multilinear Interpolation Technique and Simplex Algorithm</title><title>Journal of computational chemistry</title><addtitle>J Comput Chem</addtitle><description>A fast, reasonable, and transferable coarse‐grained (CG) molecular dynamics force field (FF) is essential to combine experimental and simulation data. However, the parameterization of CG FF usually requires massive computation, which hinders its rapid development. Here, we presented an efficient optimization protocol by combining multilinear interpolation technique with simplex algorithm. In this preliminary work, taking the experimental properties as the benchmark, we constructed a new set of CG FF for water and n‐alkanes by adopting piecewise Morse function to describe the nonbonded interactions. This CG FF has a delicate balance between efficiency, accuracy, and transferability and well reproduced the correct structural and thermodynamics properties of pure water and alkane liquids. More importantly, optimized Morse potential was also successfully applied to describe the interactions between water and n‐alkanes. It nicely predicted the phase separation, interface tension, hydration free energy, and formation of microemulsions of water/oil mixtures. © 2019 Wiley Periodicals, Inc.
The combination of global search and local refinement is essential in complex force field development. Here, the authors presented a global multilinear interpolation method (MIP) that is fast and easy to be implemented. As a demo, the authors combined MIP with a local simplex algorithm to develop efficient, accurate, and transferrable coarse‐grained force fields for water and alkanes. Routine of MIP combined with simplex.</description><subject>Algorithms</subject><subject>Alkanes</subject><subject>Coarsening</subject><subject>coarse‐grained force field</subject><subject>Computer simulation</subject><subject>Free energy</subject><subject>hydrocarbon</subject><subject>Interpolation</subject><subject>Microemulsions</subject><subject>Molecular dynamics</subject><subject>Morse potential</subject><subject>multilinear interpolation</subject><subject>Optimization</subject><subject>Parameterization</subject><subject>Phase separation</subject><subject>simplex</subject><subject>Surface tension</subject><subject>water</subject><issn>0192-8651</issn><issn>1096-987X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><recordid>eNp10c1u1DAUBWALgehQWPACyBIbWKS1ffPnZZUypaiIBUViFzn2TeuRYwc7AWbHI_CMPAmGKSyQWN2FPx0d-RDylLMTzpg43Wl9ImoO_B7ZcCbrQrbNx_tkw7gURVtX_Ig8SmnHGIOqLh-SI-BtJUGKDYnn-BldmCf0Cw0j7YKKCX98-34RlfVo6DZEjXRr0Rk67PP7NFhv_Q19u7rFumxUpJd-wTgHpxYbPL1GfevtpxWp8oa-t9Ps8Cs9czch2uV2ekwejMolfHJ3j8mH7avr7nVx9e7isju7KjRUwAsO0MiWNS2oSg9mNCBrVTWIvNal0iafoRTlaBCAswFK3bZQmZHLZtCiLOGYvDjkzjHkMmnpJ5s0Oqc8hjX1AoRsoKlLyPT5P3QX1uhzu6wqLlqWG2X18qB0DClFHPs52knFfc9Z_2uIPg_R_x4i22d3ieswofkr__x8BqcH8MU63P8_qX_TdYfInwDokwM</recordid><startdate>20200330</startdate><enddate>20200330</enddate><creator>Wan, Mingwei</creator><creator>Song, Junjie</creator><creator>Li, Wenli</creator><creator>Gao, Lianghui</creator><creator>Fang, Weihai</creator><general>John Wiley & Sons, Inc</general><general>Wiley Subscription Services, Inc</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>JQ2</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0003-4414-3671</orcidid><orcidid>https://orcid.org/0000-0002-1668-465X</orcidid></search><sort><creationdate>20200330</creationdate><title>Development of Coarse‐Grained Force Field by Combining Multilinear Interpolation Technique and Simplex Algorithm</title><author>Wan, Mingwei ; Song, Junjie ; Li, Wenli ; Gao, Lianghui ; Fang, Weihai</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3531-1337980783a5cbdfd396a57ee16c4acd16cb424fde3310b34c8835df197bc2443</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Algorithms</topic><topic>Alkanes</topic><topic>Coarsening</topic><topic>coarse‐grained force field</topic><topic>Computer simulation</topic><topic>Free energy</topic><topic>hydrocarbon</topic><topic>Interpolation</topic><topic>Microemulsions</topic><topic>Molecular dynamics</topic><topic>Morse potential</topic><topic>multilinear interpolation</topic><topic>Optimization</topic><topic>Parameterization</topic><topic>Phase separation</topic><topic>simplex</topic><topic>Surface tension</topic><topic>water</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wan, Mingwei</creatorcontrib><creatorcontrib>Song, Junjie</creatorcontrib><creatorcontrib>Li, Wenli</creatorcontrib><creatorcontrib>Gao, Lianghui</creatorcontrib><creatorcontrib>Fang, Weihai</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Computer Science Collection</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of computational chemistry</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wan, Mingwei</au><au>Song, Junjie</au><au>Li, Wenli</au><au>Gao, Lianghui</au><au>Fang, Weihai</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Development of Coarse‐Grained Force Field by Combining Multilinear Interpolation Technique and Simplex Algorithm</atitle><jtitle>Journal of computational chemistry</jtitle><addtitle>J Comput Chem</addtitle><date>2020-03-30</date><risdate>2020</risdate><volume>41</volume><issue>8</issue><spage>814</spage><epage>829</epage><pages>814-829</pages><issn>0192-8651</issn><eissn>1096-987X</eissn><abstract>A fast, reasonable, and transferable coarse‐grained (CG) molecular dynamics force field (FF) is essential to combine experimental and simulation data. However, the parameterization of CG FF usually requires massive computation, which hinders its rapid development. Here, we presented an efficient optimization protocol by combining multilinear interpolation technique with simplex algorithm. In this preliminary work, taking the experimental properties as the benchmark, we constructed a new set of CG FF for water and n‐alkanes by adopting piecewise Morse function to describe the nonbonded interactions. This CG FF has a delicate balance between efficiency, accuracy, and transferability and well reproduced the correct structural and thermodynamics properties of pure water and alkane liquids. More importantly, optimized Morse potential was also successfully applied to describe the interactions between water and n‐alkanes. It nicely predicted the phase separation, interface tension, hydration free energy, and formation of microemulsions of water/oil mixtures. © 2019 Wiley Periodicals, Inc.
The combination of global search and local refinement is essential in complex force field development. Here, the authors presented a global multilinear interpolation method (MIP) that is fast and easy to be implemented. As a demo, the authors combined MIP with a local simplex algorithm to develop efficient, accurate, and transferrable coarse‐grained force fields for water and alkanes. Routine of MIP combined with simplex.</abstract><cop>Hoboken, USA</cop><pub>John Wiley & Sons, Inc</pub><pmid>31859392</pmid><doi>10.1002/jcc.26131</doi><tpages>16</tpages><orcidid>https://orcid.org/0000-0003-4414-3671</orcidid><orcidid>https://orcid.org/0000-0002-1668-465X</orcidid></addata></record> |
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subjects | Algorithms Alkanes Coarsening coarse‐grained force field Computer simulation Free energy hydrocarbon Interpolation Microemulsions Molecular dynamics Morse potential multilinear interpolation Optimization Parameterization Phase separation simplex Surface tension water |
title | Development of Coarse‐Grained Force Field by Combining Multilinear Interpolation Technique and Simplex Algorithm |
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