| Maintain rigid structures in Verlet based cartesian molecular dynamics simulations. | |
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MedLine Citation:
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PMID: 23039588 Owner: NLM Status: MEDLINE |
Abstract/OtherAbstract:
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An algorithm is presented to maintain rigid structures in Verlet based cartesian molecular dynamics (MD) simulations. After each unconstrained MD step, the coordinates of selected particles are corrected to maintain rigid structures through an iterative procedure of rotation matrix computation. This algorithm, named as SHAPE and implemented in CHARMM program suite, avoids the calculations of Lagrange multipliers, so that the complexity of computation does not increase with the number of particles in a rigid structure. The implementation of this algorithm does not require significant modification of propagation integrator, and can be plugged into any cartesian based MD integration scheme. A unique feature of the SHAPE method is that it is interchangeable with SHAKE for any object that can be constrained as a rigid structure using multiple SHAKE constraints. Unlike SHAKE, the SHAPE method can be applied to large linear (with three or more centers) and planar (with four or more centers) rigid bodies. Numerical tests with four model systems including two proteins demonstrate that the accuracy and reliability of the SHAPE method are comparable to the SHAKE method, but with much more applicability and efficiency. |
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Authors:
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Peng Tao; Xiongwu Wu; Bernard R Brooks |
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Publication Detail:
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Type: Journal Article; Research Support, N.I.H., Intramural |
Journal Detail:
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Title: The Journal of chemical physics Volume: 137 ISSN: 1089-7690 ISO Abbreviation: J Chem Phys Publication Date: 2012 Oct |
Date Detail:
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Created Date: 2012-10-08 Completed Date: 2013-02-20 Revised Date: 2013-04-16 |
Medline Journal Info:
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Nlm Unique ID: 0375360 Medline TA: J Chem Phys Country: United States |
Other Details:
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Languages: eng Pagination: 134110 Citation Subset: IM |
Affiliation:
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Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA. |
Export Citation:
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| MeSH Terms | |
Descriptor/Qualifier:
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Algorithms Models, Molecular Molecular Conformation Molecular Dynamics Simulation* Peptides / chemistry* Proteins / chemistry* Water / chemistry* |
| Chemical | |
Reg. No./Substance:
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0/Peptides; 0/Proteins; 7732-18-5/Water |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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