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.
Keywords: Coarse grain; GROMACS; Lipopolysaccharide; MARTINI; Molecular dynamics; P. aeruginosa; POPE.
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