Loading…

On the calculation of free energies over Hamiltonian and order parameters via perturbation and thermodynamic integration

In this work, complementary formulas are presented to compute free-energy differences via perturbation (FEP) methods and thermodynamic integration (TI). These formulas are derived by selecting only the most statistically significant data from the information extractable from the simulated points inv...

Full description

Saved in:
Bibliographic Details
Published in:The Journal of chemical physics 2021-09, Vol.155 (11), p.114112-114112
Main Author: Escobedo, Fernando A.
Format: Article
Language:English
Subjects:
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
cited_by cdi_FETCH-LOGICAL-c325t-ac5113adbe9f497dce1973dd2c9aae0b1f3681dd552ed19e24471f521f711ef43
cites cdi_FETCH-LOGICAL-c325t-ac5113adbe9f497dce1973dd2c9aae0b1f3681dd552ed19e24471f521f711ef43
container_end_page 114112
container_issue 11
container_start_page 114112
container_title The Journal of chemical physics
container_volume 155
creator Escobedo, Fernando A.
description In this work, complementary formulas are presented to compute free-energy differences via perturbation (FEP) methods and thermodynamic integration (TI). These formulas are derived by selecting only the most statistically significant data from the information extractable from the simulated points involved. On the one hand, commonly used FEP techniques based on overlap sampling leverage the full information contained in the overlapping macrostate probability distributions. On the other hand, conventional TI methods only use information on the first moments of those distributions, as embodied by the first derivatives of the free energy. Since the accuracy of simulation data degrades considerably for high-order moments (for FEP) or free-energy derivatives (for TI), it is proposed to consider, consistently for both methods, data up to second-order moments/derivatives. This provides a compromise between the limiting strategies embodied by common FEP and TI and leads to simple, optimized expressions to evaluate free-energy differences. The proposed formulas are validated with an analytically solvable harmonic Hamiltonian (for assessing systematic errors), an atomistic system (for computing the potential of mean force with coordinate-dependent order parameters), and a binary-component coarse-grained model (for tracing a solid–liquid phase diagram in an ensemble sampled through alchemical transformations). It is shown that the proposed FEP and TI formulas are straightforward to implement, perform similarly well, and allow robust estimation of free-energy differences even when the spacing of successive points does not guarantee them to have proper overlapping in phase space.
doi_str_mv 10.1063/5.0061541
format article
fullrecord <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_crossref_primary_10_1063_5_0061541</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2575835753</sourcerecordid><originalsourceid>FETCH-LOGICAL-c325t-ac5113adbe9f497dce1973dd2c9aae0b1f3681dd552ed19e24471f521f711ef43</originalsourceid><addsrcrecordid>eNp90UtLxDAQB_AgCq6Pg98g4EWFaiZt-jiK-IKFvei5ZJPJmqVN1iQV99vb3Xry4CWB5Dd_ZhhCLoDdAivzO3HLWAmigAMyA1Y3WVU27JDMGOOQNSUrj8lJjGvGGFS8mJHvhaPpA6mSnRo6max31BtqAiJFh2FlMVL_hYG-yN52yTsrHZVOUx_0-LqRQfaYMET6ZSXdYEhDWE45OzVmh97rrRurFbUu4Srsf8_IkZFdxPPf-5S8Pz2-Pbxk88Xz68P9PFM5FymTSgDkUi-xMUVTaYXQVLnWXDVSIluCycsatBaCo4YGeVFUYAQHUwGgKfJTcjXlboL_HDCmtrdRYddJh36ILReVqPPxyEd6-Yeu_RDc2N1OFQLKuuSjup6UCj7GgKbdBNvLsG2BtbsdtKL93cFobyYblU37sf_BP448iAc</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2574516862</pqid></control><display><type>article</type><title>On the calculation of free energies over Hamiltonian and order parameters via perturbation and thermodynamic integration</title><source>American Institute of Physics:Jisc Collections:Transitional Journals Agreement 2021-23 (Reading list)</source><source>AIP_美国物理联合会现刊(与NSTL共建)</source><creator>Escobedo, Fernando A.</creator><creatorcontrib>Escobedo, Fernando A.</creatorcontrib><description>In this work, complementary formulas are presented to compute free-energy differences via perturbation (FEP) methods and thermodynamic integration (TI). These formulas are derived by selecting only the most statistically significant data from the information extractable from the simulated points involved. On the one hand, commonly used FEP techniques based on overlap sampling leverage the full information contained in the overlapping macrostate probability distributions. On the other hand, conventional TI methods only use information on the first moments of those distributions, as embodied by the first derivatives of the free energy. Since the accuracy of simulation data degrades considerably for high-order moments (for FEP) or free-energy derivatives (for TI), it is proposed to consider, consistently for both methods, data up to second-order moments/derivatives. This provides a compromise between the limiting strategies embodied by common FEP and TI and leads to simple, optimized expressions to evaluate free-energy differences. The proposed formulas are validated with an analytically solvable harmonic Hamiltonian (for assessing systematic errors), an atomistic system (for computing the potential of mean force with coordinate-dependent order parameters), and a binary-component coarse-grained model (for tracing a solid–liquid phase diagram in an ensemble sampled through alchemical transformations). It is shown that the proposed FEP and TI formulas are straightforward to implement, perform similarly well, and allow robust estimation of free-energy differences even when the spacing of successive points does not guarantee them to have proper overlapping in phase space.</description><identifier>ISSN: 0021-9606</identifier><identifier>EISSN: 1089-7690</identifier><identifier>DOI: 10.1063/5.0061541</identifier><identifier>CODEN: JCPSA6</identifier><language>eng</language><publisher>Melville: American Institute of Physics</publisher><subject>Free energy ; Liquid phases ; Order parameters ; Perturbation ; Phase diagrams ; Systematic errors</subject><ispartof>The Journal of chemical physics, 2021-09, Vol.155 (11), p.114112-114112</ispartof><rights>Author(s)</rights><rights>2021 Author(s). Published under an exclusive license by AIP Publishing.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c325t-ac5113adbe9f497dce1973dd2c9aae0b1f3681dd552ed19e24471f521f711ef43</citedby><cites>FETCH-LOGICAL-c325t-ac5113adbe9f497dce1973dd2c9aae0b1f3681dd552ed19e24471f521f711ef43</cites><orcidid>0000-0002-4722-9836</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://pubs.aip.org/jcp/article-lookup/doi/10.1063/5.0061541$$EHTML$$P50$$Gscitation$$H</linktohtml><link.rule.ids>314,780,782,784,795,27924,27925,76383</link.rule.ids></links><search><creatorcontrib>Escobedo, Fernando A.</creatorcontrib><title>On the calculation of free energies over Hamiltonian and order parameters via perturbation and thermodynamic integration</title><title>The Journal of chemical physics</title><description>In this work, complementary formulas are presented to compute free-energy differences via perturbation (FEP) methods and thermodynamic integration (TI). These formulas are derived by selecting only the most statistically significant data from the information extractable from the simulated points involved. On the one hand, commonly used FEP techniques based on overlap sampling leverage the full information contained in the overlapping macrostate probability distributions. On the other hand, conventional TI methods only use information on the first moments of those distributions, as embodied by the first derivatives of the free energy. Since the accuracy of simulation data degrades considerably for high-order moments (for FEP) or free-energy derivatives (for TI), it is proposed to consider, consistently for both methods, data up to second-order moments/derivatives. This provides a compromise between the limiting strategies embodied by common FEP and TI and leads to simple, optimized expressions to evaluate free-energy differences. The proposed formulas are validated with an analytically solvable harmonic Hamiltonian (for assessing systematic errors), an atomistic system (for computing the potential of mean force with coordinate-dependent order parameters), and a binary-component coarse-grained model (for tracing a solid–liquid phase diagram in an ensemble sampled through alchemical transformations). It is shown that the proposed FEP and TI formulas are straightforward to implement, perform similarly well, and allow robust estimation of free-energy differences even when the spacing of successive points does not guarantee them to have proper overlapping in phase space.</description><subject>Free energy</subject><subject>Liquid phases</subject><subject>Order parameters</subject><subject>Perturbation</subject><subject>Phase diagrams</subject><subject>Systematic errors</subject><issn>0021-9606</issn><issn>1089-7690</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><recordid>eNp90UtLxDAQB_AgCq6Pg98g4EWFaiZt-jiK-IKFvei5ZJPJmqVN1iQV99vb3Xry4CWB5Dd_ZhhCLoDdAivzO3HLWAmigAMyA1Y3WVU27JDMGOOQNSUrj8lJjGvGGFS8mJHvhaPpA6mSnRo6max31BtqAiJFh2FlMVL_hYG-yN52yTsrHZVOUx_0-LqRQfaYMET6ZSXdYEhDWE45OzVmh97rrRurFbUu4Srsf8_IkZFdxPPf-5S8Pz2-Pbxk88Xz68P9PFM5FymTSgDkUi-xMUVTaYXQVLnWXDVSIluCycsatBaCo4YGeVFUYAQHUwGgKfJTcjXlboL_HDCmtrdRYddJh36ILReVqPPxyEd6-Yeu_RDc2N1OFQLKuuSjup6UCj7GgKbdBNvLsG2BtbsdtKL93cFobyYblU37sf_BP448iAc</recordid><startdate>20210921</startdate><enddate>20210921</enddate><creator>Escobedo, Fernando A.</creator><general>American Institute of Physics</general><scope>AAYXX</scope><scope>CITATION</scope><scope>8FD</scope><scope>H8D</scope><scope>L7M</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-4722-9836</orcidid></search><sort><creationdate>20210921</creationdate><title>On the calculation of free energies over Hamiltonian and order parameters via perturbation and thermodynamic integration</title><author>Escobedo, Fernando A.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c325t-ac5113adbe9f497dce1973dd2c9aae0b1f3681dd552ed19e24471f521f711ef43</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Free energy</topic><topic>Liquid phases</topic><topic>Order parameters</topic><topic>Perturbation</topic><topic>Phase diagrams</topic><topic>Systematic errors</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Escobedo, Fernando A.</creatorcontrib><collection>CrossRef</collection><collection>Technology Research Database</collection><collection>Aerospace Database</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>MEDLINE - Academic</collection><jtitle>The Journal of chemical physics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Escobedo, Fernando A.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>On the calculation of free energies over Hamiltonian and order parameters via perturbation and thermodynamic integration</atitle><jtitle>The Journal of chemical physics</jtitle><date>2021-09-21</date><risdate>2021</risdate><volume>155</volume><issue>11</issue><spage>114112</spage><epage>114112</epage><pages>114112-114112</pages><issn>0021-9606</issn><eissn>1089-7690</eissn><coden>JCPSA6</coden><abstract>In this work, complementary formulas are presented to compute free-energy differences via perturbation (FEP) methods and thermodynamic integration (TI). These formulas are derived by selecting only the most statistically significant data from the information extractable from the simulated points involved. On the one hand, commonly used FEP techniques based on overlap sampling leverage the full information contained in the overlapping macrostate probability distributions. On the other hand, conventional TI methods only use information on the first moments of those distributions, as embodied by the first derivatives of the free energy. Since the accuracy of simulation data degrades considerably for high-order moments (for FEP) or free-energy derivatives (for TI), it is proposed to consider, consistently for both methods, data up to second-order moments/derivatives. This provides a compromise between the limiting strategies embodied by common FEP and TI and leads to simple, optimized expressions to evaluate free-energy differences. The proposed formulas are validated with an analytically solvable harmonic Hamiltonian (for assessing systematic errors), an atomistic system (for computing the potential of mean force with coordinate-dependent order parameters), and a binary-component coarse-grained model (for tracing a solid–liquid phase diagram in an ensemble sampled through alchemical transformations). It is shown that the proposed FEP and TI formulas are straightforward to implement, perform similarly well, and allow robust estimation of free-energy differences even when the spacing of successive points does not guarantee them to have proper overlapping in phase space.</abstract><cop>Melville</cop><pub>American Institute of Physics</pub><doi>10.1063/5.0061541</doi><tpages>18</tpages><orcidid>https://orcid.org/0000-0002-4722-9836</orcidid></addata></record>
fulltext fulltext
identifier ISSN: 0021-9606
ispartof The Journal of chemical physics, 2021-09, Vol.155 (11), p.114112-114112
issn 0021-9606
1089-7690
language eng
recordid cdi_crossref_primary_10_1063_5_0061541
source American Institute of Physics:Jisc Collections:Transitional Journals Agreement 2021-23 (Reading list); AIP_美国物理联合会现刊(与NSTL共建)
subjects Free energy
Liquid phases
Order parameters
Perturbation
Phase diagrams
Systematic errors
title On the calculation of free energies over Hamiltonian and order parameters via perturbation and thermodynamic integration
url http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-05T12%3A51%3A41IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_cross&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=On%20the%20calculation%20of%20free%20energies%20over%20Hamiltonian%20and%20order%20parameters%20via%20perturbation%20and%20thermodynamic%20integration&rft.jtitle=The%20Journal%20of%20chemical%20physics&rft.au=Escobedo,%20Fernando%20A.&rft.date=2021-09-21&rft.volume=155&rft.issue=11&rft.spage=114112&rft.epage=114112&rft.pages=114112-114112&rft.issn=0021-9606&rft.eissn=1089-7690&rft.coden=JCPSA6&rft_id=info:doi/10.1063/5.0061541&rft_dat=%3Cproquest_cross%3E2575835753%3C/proquest_cross%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c325t-ac5113adbe9f497dce1973dd2c9aae0b1f3681dd552ed19e24471f521f711ef43%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=2574516862&rft_id=info:pmid/&rfr_iscdi=true