Journal
JOURNAL OF MOLECULAR GRAPHICS & MODELLING
Volume 63, Issue -, Pages 125-133Publisher
ELSEVIER SCIENCE INC
DOI: 10.1016/j.jmgm.2015.12.002
Keywords
Lipopolysaccharide; POPE; MARTINI; Coarse grain; GROMACS; P. aeruginosa; Molecular dynamics
Categories
Funding
- Natural Sciences and Engineering Research Council of Canada
- Shared Hierarchical Academic Research Computing Network (SHARCNET)
- Compute/Calcul Canada
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We report a course-grained, large scale simulation of the outer membrane from Pseudomonas aeruginosa. Using the MARTINI force field approach of 4-to-1 atom mapping, we simulate an asymmetrically constructed bilayer with over 1100 rough lipopolysaccharide (LPS) and 3100 16:0-18:1-phosphatidylethanolamine. We achieve 90-fold improvement in computational efficiency on a system much larger than reasonable for all-atom simulation. We also compare a coarse-grained LPS/LPS bilayer simulation with known parameters determined from neutron diffraction. (C) 2015 Elsevier Inc. All rights reserved.
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