“Swarm relaxation”: Equilibrating a large ensemble of computer simulations
. It is common practice in molecular dynamics and Monte Carlo computer simulations to run multiple, separately-initialized simulations in order to improve the sampling of independent microstates. Here we examine the utility of an extreme case of this strategy, in which we run a large ensemble of M i...
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Veröffentlicht in: | The European physical journal. E, Soft matter and biological physics Soft matter and biological physics, 2017-11, Vol.40 (11), p.98-11, Article 98 |
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creator | Malek, Shahrazad M. A. Bowles, Richard K. Saika-Voivod, Ivan Sciortino, Francesco Poole, Peter H. |
description | .
It is common practice in molecular dynamics and Monte Carlo computer simulations to run multiple, separately-initialized simulations in order to improve the sampling of independent microstates. Here we examine the utility of an extreme case of this strategy, in which we run a large ensemble of
M
independent simulations (a “swarm”), each of which is relaxed to equilibrium. We show that if
M
is of order
10
3
, we can monitor the swarm’s relaxation to equilibrium, and confirm its attainment, within
∼
10
τ
¯
, where
τ
¯
is the equilibrium relaxation time. As soon as a swarm of this size attains equilibrium, the ensemble of
M
final microstates from each run is sufficient for the evaluation of most equilibrium properties without further sampling. This approach dramatically reduces the wall-clock time required, compared to a single long simulation, by a factor of several hundred, at the cost of an increase in the total computational effort by a small factor. It is also well suited to modern computing systems having thousands of processors, and is a viable strategy for simulation studies that need to produce high-precision results in a minimum of wall-clock time. We present results obtained by applying this approach to several test cases.
Graphical abstract |
doi_str_mv | 10.1140/epje/i2017-11588-2 |
format | Article |
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It is common practice in molecular dynamics and Monte Carlo computer simulations to run multiple, separately-initialized simulations in order to improve the sampling of independent microstates. Here we examine the utility of an extreme case of this strategy, in which we run a large ensemble of
M
independent simulations (a “swarm”), each of which is relaxed to equilibrium. We show that if
M
is of order
10
3
, we can monitor the swarm’s relaxation to equilibrium, and confirm its attainment, within
∼
10
τ
¯
, where
τ
¯
is the equilibrium relaxation time. As soon as a swarm of this size attains equilibrium, the ensemble of
M
final microstates from each run is sufficient for the evaluation of most equilibrium properties without further sampling. This approach dramatically reduces the wall-clock time required, compared to a single long simulation, by a factor of several hundred, at the cost of an increase in the total computational effort by a small factor. It is also well suited to modern computing systems having thousands of processors, and is a viable strategy for simulation studies that need to produce high-precision results in a minimum of wall-clock time. We present results obtained by applying this approach to several test cases.
Graphical abstract</description><identifier>ISSN: 1292-8941</identifier><identifier>EISSN: 1292-895X</identifier><identifier>DOI: 10.1140/epje/i2017-11588-2</identifier><identifier>PMID: 29119281</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Advances in Computational Methods for Soft Matter Systems ; Biological and Medical Physics ; Biophysics ; Complex Fluids and Microfluidics ; Complex Systems ; Computer simulation ; Condensed matter physics ; Equilibrium ; Molecular dynamics ; Nanotechnology ; Physics ; Physics and Astronomy ; Polymer Sciences ; Processors ; Regular Article ; Relaxation time ; Sampling ; Simulation ; Soft and Granular Matter ; Surfaces and Interfaces ; Thin Films</subject><ispartof>The European physical journal. E, Soft matter and biological physics, 2017-11, Vol.40 (11), p.98-11, Article 98</ispartof><rights>EDP Sciences, SIF, Springer-Verlag GmbH Germany, part of Springer Nature 2017</rights><rights>Copyright Springer Science & Business Media 2017</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c375t-cc191d05a7d3af646074557be6809d640b261cfba5192cb414c473e17dee54883</citedby><cites>FETCH-LOGICAL-c375t-cc191d05a7d3af646074557be6809d640b261cfba5192cb414c473e17dee54883</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1140/epje/i2017-11588-2$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1140/epje/i2017-11588-2$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/29119281$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Malek, Shahrazad M. A.</creatorcontrib><creatorcontrib>Bowles, Richard K.</creatorcontrib><creatorcontrib>Saika-Voivod, Ivan</creatorcontrib><creatorcontrib>Sciortino, Francesco</creatorcontrib><creatorcontrib>Poole, Peter H.</creatorcontrib><title>“Swarm relaxation”: Equilibrating a large ensemble of computer simulations</title><title>The European physical journal. E, Soft matter and biological physics</title><addtitle>Eur. Phys. J. E</addtitle><addtitle>Eur Phys J E Soft Matter</addtitle><description>.
It is common practice in molecular dynamics and Monte Carlo computer simulations to run multiple, separately-initialized simulations in order to improve the sampling of independent microstates. Here we examine the utility of an extreme case of this strategy, in which we run a large ensemble of
M
independent simulations (a “swarm”), each of which is relaxed to equilibrium. We show that if
M
is of order
10
3
, we can monitor the swarm’s relaxation to equilibrium, and confirm its attainment, within
∼
10
τ
¯
, where
τ
¯
is the equilibrium relaxation time. As soon as a swarm of this size attains equilibrium, the ensemble of
M
final microstates from each run is sufficient for the evaluation of most equilibrium properties without further sampling. This approach dramatically reduces the wall-clock time required, compared to a single long simulation, by a factor of several hundred, at the cost of an increase in the total computational effort by a small factor. It is also well suited to modern computing systems having thousands of processors, and is a viable strategy for simulation studies that need to produce high-precision results in a minimum of wall-clock time. We present results obtained by applying this approach to several test cases.
Graphical abstract</description><subject>Advances in Computational Methods for Soft Matter Systems</subject><subject>Biological and Medical Physics</subject><subject>Biophysics</subject><subject>Complex Fluids and Microfluidics</subject><subject>Complex Systems</subject><subject>Computer simulation</subject><subject>Condensed matter physics</subject><subject>Equilibrium</subject><subject>Molecular dynamics</subject><subject>Nanotechnology</subject><subject>Physics</subject><subject>Physics and Astronomy</subject><subject>Polymer Sciences</subject><subject>Processors</subject><subject>Regular Article</subject><subject>Relaxation time</subject><subject>Sampling</subject><subject>Simulation</subject><subject>Soft and Granular Matter</subject><subject>Surfaces and Interfaces</subject><subject>Thin Films</subject><issn>1292-8941</issn><issn>1292-895X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><recordid>eNp1kMtKAzEUhoMotlZfwIUMuHEzNieTzMWdlHqBogsV3IVM5kyZMrcmHdRdH0Rfrk_iTFuLCK4Sku__z-Ej5BToJQCnQ6xnOMwYhcAFEGHosj3SBxYxN4zE6_7uzqFHjqydUUrbmHdIeiwCiFgIffKwWn4-vSlTOAZz9a4WWVWull9XznjeZHkWm_alnDrKyZWZooOlxSLO0alSR1dF3SzQODYrmnydtMfkIFW5xZPtOSAvN-Pn0Z07eby9H11PXO0FYuFqDREkVKgg8VTqc58GXIggRj-kUeJzGjMfdBor0a6pYw5c88BDCBJEwcPQG5CLTW9tqnmDdiGLzGrMc1Vi1VgJkc84ExCwFj3_g86qxpTtdh0FoSc4jVqKbShtKmsNprI2WaHMhwQqO9uysy3XtuXatuyqz7bVTVxgsov86G0BbwPY9qucovk1-__ab86kjdo</recordid><startdate>20171110</startdate><enddate>20171110</enddate><creator>Malek, Shahrazad M. A.</creator><creator>Bowles, Richard K.</creator><creator>Saika-Voivod, Ivan</creator><creator>Sciortino, Francesco</creator><creator>Poole, Peter H.</creator><general>Springer Berlin Heidelberg</general><general>Springer Nature B.V</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>20171110</creationdate><title>“Swarm relaxation”: Equilibrating a large ensemble of computer simulations</title><author>Malek, Shahrazad M. A. ; Bowles, Richard K. ; Saika-Voivod, Ivan ; Sciortino, Francesco ; Poole, Peter H.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c375t-cc191d05a7d3af646074557be6809d640b261cfba5192cb414c473e17dee54883</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Advances in Computational Methods for Soft Matter Systems</topic><topic>Biological and Medical Physics</topic><topic>Biophysics</topic><topic>Complex Fluids and Microfluidics</topic><topic>Complex Systems</topic><topic>Computer simulation</topic><topic>Condensed matter physics</topic><topic>Equilibrium</topic><topic>Molecular dynamics</topic><topic>Nanotechnology</topic><topic>Physics</topic><topic>Physics and Astronomy</topic><topic>Polymer Sciences</topic><topic>Processors</topic><topic>Regular Article</topic><topic>Relaxation time</topic><topic>Sampling</topic><topic>Simulation</topic><topic>Soft and Granular Matter</topic><topic>Surfaces and Interfaces</topic><topic>Thin Films</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Malek, Shahrazad M. A.</creatorcontrib><creatorcontrib>Bowles, Richard K.</creatorcontrib><creatorcontrib>Saika-Voivod, Ivan</creatorcontrib><creatorcontrib>Sciortino, Francesco</creatorcontrib><creatorcontrib>Poole, Peter H.</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>The European physical journal. E, Soft matter and biological physics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Malek, Shahrazad M. A.</au><au>Bowles, Richard K.</au><au>Saika-Voivod, Ivan</au><au>Sciortino, Francesco</au><au>Poole, Peter H.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>“Swarm relaxation”: Equilibrating a large ensemble of computer simulations</atitle><jtitle>The European physical journal. E, Soft matter and biological physics</jtitle><stitle>Eur. Phys. J. E</stitle><addtitle>Eur Phys J E Soft Matter</addtitle><date>2017-11-10</date><risdate>2017</risdate><volume>40</volume><issue>11</issue><spage>98</spage><epage>11</epage><pages>98-11</pages><artnum>98</artnum><issn>1292-8941</issn><eissn>1292-895X</eissn><abstract>.
It is common practice in molecular dynamics and Monte Carlo computer simulations to run multiple, separately-initialized simulations in order to improve the sampling of independent microstates. Here we examine the utility of an extreme case of this strategy, in which we run a large ensemble of
M
independent simulations (a “swarm”), each of which is relaxed to equilibrium. We show that if
M
is of order
10
3
, we can monitor the swarm’s relaxation to equilibrium, and confirm its attainment, within
∼
10
τ
¯
, where
τ
¯
is the equilibrium relaxation time. As soon as a swarm of this size attains equilibrium, the ensemble of
M
final microstates from each run is sufficient for the evaluation of most equilibrium properties without further sampling. This approach dramatically reduces the wall-clock time required, compared to a single long simulation, by a factor of several hundred, at the cost of an increase in the total computational effort by a small factor. It is also well suited to modern computing systems having thousands of processors, and is a viable strategy for simulation studies that need to produce high-precision results in a minimum of wall-clock time. We present results obtained by applying this approach to several test cases.
Graphical abstract</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><pmid>29119281</pmid><doi>10.1140/epje/i2017-11588-2</doi><tpages>11</tpages></addata></record> |
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subjects | Advances in Computational Methods for Soft Matter Systems Biological and Medical Physics Biophysics Complex Fluids and Microfluidics Complex Systems Computer simulation Condensed matter physics Equilibrium Molecular dynamics Nanotechnology Physics Physics and Astronomy Polymer Sciences Processors Regular Article Relaxation time Sampling Simulation Soft and Granular Matter Surfaces and Interfaces Thin Films |
title | “Swarm relaxation”: Equilibrating a large ensemble of computer simulations |
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