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231224s2017 xx |||||o 00| ||eng c |
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|a 10.1002/jcc.24782
|2 doi
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|a pubmed24n1348.xml
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|a (DE-627)NLM270077987
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|a (NLM)28318096
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|a DE-627
|b ger
|c DE-627
|e rakwb
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|a eng
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| 100 |
1 |
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|a Wang, Changhao
|e verfasserin
|4 aut
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| 245 |
1 |
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|a Numerical interpretation of molecular surface field in dielectric modeling of solvation
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|c 2017
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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
|b cr
|2 rdacarrier
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|a Date Completed 07.05.2019
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|a Date Revised 26.03.2024
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|a published: Print-Electronic
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|a Citation Status MEDLINE
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|a © 2017 Wiley Periodicals, Inc.
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|a Continuum solvent models, particularly those based on the Poisson-Boltzmann equation (PBE), are widely used in the studies of biomolecular structures and functions. Existing PBE developments have been mainly focused on how to obtain more accurate and/or more efficient numerical potentials and energies. However to adopt the PBE models for molecular dynamics simulations, a difficulty is how to interpret dielectric boundary forces accurately and efficiently for robust dynamics simulations. This study documents the implementation and analysis of a range of standard fitting schemes, including both one-sided and two-sided methods with both first-order and second-order Taylor expansions, to calculate molecular surface electric fields to facilitate the numerical calculation of dielectric boundary forces. These efforts prompted us to develop an efficient approximated one-dimensional method, which is to fit the surface field one dimension at a time, for biomolecular applications without much compromise in accuracy. We also developed a surface-to-atom force partition scheme given a level set representation of analytical molecular surfaces to facilitate their applications to molecular simulations. Testing of these fitting methods in the dielectric boundary force calculations shows that the second-order methods, including the one-dimensional method, consistently perform among the best in the molecular test cases. Finally, the timing analysis shows the approximated one-dimensional method is far more efficient than standard second-order methods in the PBE force calculations. © 2017 Wiley Periodicals, Inc
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|a Journal Article
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|a Research Support, N.I.H., Extramural
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|a Continuum Solvent
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4 |
|a Poisson-Boltzmann equation
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| 650 |
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|a dielectric boundary force
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4 |
|a molecular surface
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| 650 |
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7 |
|a Solvents
|2 NLM
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| 700 |
1 |
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|a Xiao, Li
|e verfasserin
|4 aut
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| 700 |
1 |
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|a Luo, Ray
|e verfasserin
|4 aut
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| 773 |
0 |
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|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 38(2017), 14 vom: 30. Mai, Seite 1057-1070
|w (DE-627)NLM098138448
|x 1096-987X
|7 nnns
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| 773 |
1 |
8 |
|g volume:38
|g year:2017
|g number:14
|g day:30
|g month:05
|g pages:1057-1070
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| 856 |
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|u http://dx.doi.org/10.1002/jcc.24782
|3 Volltext
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