Document Detail


Classical molecular dynamics in a nutshell.
MedLine Citation:
PMID:  23034748     Owner:  NLM     Status:  In-Data-Review    
Abstract/OtherAbstract:
This chapter provides an overview of the various techniques that are commonly used in classical molecular dynamics simulations. It describes suitable algorithms for the integration of Newton's equation of motion over many time steps for systems containing a large number of particles, different choices of boundary conditions as well as available force fields for biological systems, that is, the mathematical description of the interactions of atoms and molecules with each other. It also illustrates algorithms used to simulate systems at constant temperature and/or pressure and discusses their advantages and disadvantages. It presents a few methods to save CPU time and a summary of popular software for biomolecular molecular dynamics simulations.
Authors:
Susanna Hug
Related Documents :
18305698 - Micro-optical bench for alignment-free optical coupling.
24920008 - Time-dependent density functional theory for ion diffusion in electrochemical systems.
Publication Detail:
Type:  Journal Article    
Journal Detail:
Title:  Methods in molecular biology (Clifton, N.J.)     Volume:  924     ISSN:  1940-6029     ISO Abbreviation:  Methods Mol. Biol.     Publication Date:  2013  
Date Detail:
Created Date:  2012-10-04     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  9214969     Medline TA:  Methods Mol Biol     Country:  United States    
Other Details:
Languages:  eng     Pagination:  127-52     Citation Subset:  IM    
Affiliation:
Department of Applied Mathematics, University of Western Ontario, London, ON, Canada.
Export Citation:
APA/MLA Format     Download EndNote     Download BibTex
MeSH Terms
Descriptor/Qualifier:

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


Previous Document:  QM and QM/MM Simulations of Proteins.
Next Document:  Enhanced sampling algorithms.