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231223s2004 xx ||||| 00| ||eng c |
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|a (DE-627)NLM147641381
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|a (NLM)15067679
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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 Bekker, Henk
|e verfasserin
|4 aut
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|a A method to obtain a near-minimal-volume molecular simulation of a macromolecule, using periodic boundary conditions and rotational constraints
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|c 2004
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|a Text
|b txt
|2 rdacontent
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|a ohne Hilfsmittel zu benutzen
|b n
|2 rdamedia
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|a Band
|b nc
|2 rdacarrier
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|a Date Completed 09.06.2004
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|a Date Revised 06.04.2004
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|a published: Print
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|a Citation Status MEDLINE
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|a Copyright 2004 Wiley Periodicals, Inc.
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|a If the rotational motion of a single macromolecule is constrained during a molecular dynamics simulation with periodic boundary conditions it is possible to perform such simulations in a computational box with a minimal amount of solvent. In this article we describe a method to construct such a box, and test the approach on a number of macromolecules, randomly chosen from the protein databank. The essence of the method is that the molecule is first dilated with a layer of at least half the cut-off radius. For the enlarged molecule a near-densest lattice packing is calculated. From this packing the simulation box is derived. On average, the volume of the resulting box proves to be about 50% of the volume of standard boxes. In test simulations this yields on average a factor of about two in simulation speed
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|a Journal Article
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| 650 |
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|a Proteins
|2 NLM
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| 700 |
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|a van den Berg, Jur P
|e verfasserin
|4 aut
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| 700 |
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|a Wassenaar, Tsjerk A
|e verfasserin
|4 aut
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| 773 |
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|i Enthalten in
|t Journal of computational chemistry
|d 1984
|g 25(2004), 8 vom: 27. Juni, Seite 1037-46
|w (DE-627)NLM098138448
|x 1096-987X
|7 nnns
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| 773 |
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|g volume:25
|g year:2004
|g number:8
|g day:27
|g month:06
|g pages:1037-46
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|a GBV_ILN_350
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|a AR
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|d 25
|j 2004
|e 8
|b 27
|c 06
|h 1037-46
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