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231225s2021 xx |||||o 00| ||eng c |
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|a 10.1002/jcc.26545
|2 doi
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|a pubmed25n1084.xml
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|a (DE-627)NLM325290679
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|a (NLM)33977553
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|a DE-627
|b ger
|c DE-627
|e rakwb
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|a eng
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|a Prasad, Samarjeet
|e verfasserin
|4 aut
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|a The Extended Eighth-Shell method for periodic boundary conditions with rotational symmetry
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|c 2021
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|a Text
|b txt
|2 rdacontent
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|a ƒaComputermedien
|b c
|2 rdamedia
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|a ƒa Online-Ressource
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|2 rdacarrier
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|a Date Completed 29.11.2021
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|a Date Revised 29.11.2021
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|a published: Print-Electronic
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|a Citation Status MEDLINE
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|a Published 2021. This article is a U.S. Government work and is in the public domain in the USA.
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|a The Eighth-Shell method for parallelization of molecular dynamics simulations has previously been shown to be the most optimal for efficiency at large process counts. However, in its current formulation only the P1 space group is supported for periodic boundary conditions (PBC) and thus reflection and/or rotational crystal symmetries are not supported. In this work, we outline the development and implementation of the Extended Eighth-Shell (EES) method that allows rotational symmetry by using an extended import region compared to the ES method. It simulates only the asymmetric unit and communicates coordinates and forces with images that correspond to P21 PBC. The P21 PBC has application in lipid bilayer simulations as it can be used to allow lipids to switch leaftlets, thus rapidly balancing the chemical potential difference between the two layers. Our results show that the EES method scales efficiently over large number of processes and can be used for simulations with P21 symmetry in an orthorhombic crystal
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|a Journal Article
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|a Research Support, N.I.H., Intramural
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|a CHARMM
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|a Eighth-Shell method
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|a Extended Eighth-Shell method
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|a P21 periodic boundary conditions
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|a domain decomposition
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| 650 |
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|a high performance computing
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| 650 |
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4 |
|a lipid simulations
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| 650 |
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|a Lipid Bilayers
|2 NLM
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| 650 |
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|a Lipids
|2 NLM
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1 |
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|a Simmonett, Andrew C
|e verfasserin
|4 aut
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1 |
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|a Meana-Pañeda, Rubén
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Brooks, Bernard R
|e verfasserin
|4 aut
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| 773 |
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|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 42(2021), 19 vom: 15. Juli, Seite 1373-1383
|w (DE-627)NLM098138448
|x 1096-987X
|7 nnas
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| 773 |
1 |
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|g volume:42
|g year:2021
|g number:19
|g day:15
|g month:07
|g pages:1373-1383
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|u http://dx.doi.org/10.1002/jcc.26545
|3 Volltext
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