Document Detail


Maintain rigid structures in Verlet based cartesian molecular dynamics simulations.
MedLine Citation:
PMID:  23039588     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
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.
Authors:
Peng Tao; Xiongwu Wu; Bernard R Brooks
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Intramural    
Journal Detail:
Title:  The Journal of chemical physics     Volume:  137     ISSN:  1089-7690     ISO Abbreviation:  J Chem Phys     Publication Date:  2012 Oct 
Date Detail:
Created Date:  2012-10-08     Completed Date:  2013-02-20     Revised Date:  2013-10-17    
Medline Journal Info:
Nlm Unique ID:  0375360     Medline TA:  J Chem Phys     Country:  United States    
Other Details:
Languages:  eng     Pagination:  134110     Citation Subset:  IM    
Affiliation:
Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
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MeSH Terms
Descriptor/Qualifier:
Algorithms
Models, Molecular
Molecular Conformation
Molecular Dynamics Simulation*
Peptides / chemistry*
Proteins / chemistry*
Water / chemistry*
Chemical
Reg. No./Substance:
0/Peptides; 0/Proteins; 7732-18-5/Water
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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