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Headgroup Conformations of Phospholipids from Molecular Dynamics Simulation: Sampling Challenges and Comparison to Experiment.
MedLine Citation:
PMID:  22159954     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
The preferred conformations of the glycerol region of a phospholipid have been explored using replica exchange molecular dynamics (MD) simulations and compared with the results of standard MD approaches and with experiment. We found that due to isomerization rates in key torsions that are slow on the timescale of atomistic MD simulations, standard MD is not able to produce accurate equilibrium conformer distributions from reasonable trajectory lengths (e.g., on the 100 ns) timescale. Replica exchange MD, however, results in quite efficient sampling due to the rapid increase in isomerization rate with temperature. The equilibrium distributions obtained from replica exchange MD have been compared with the results of experimental nuclear magnetic resonance observations. This comparison suggests that the sampling approach demonstrated here is a valuable tool that can be used in evaluating force fields for molecular simulation of lipids.
Authors:
Alexander Vogel; Scott E Feller
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2011-12-9
Journal Detail:
Title:  The Journal of membrane biology     Volume:  -     ISSN:  1432-1424     ISO Abbreviation:  -     Publication Date:  2011 Dec 
Date Detail:
Created Date:  2011-12-13     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  0211301     Medline TA:  J Membr Biol     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Affiliation:
Institute of Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany.
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