| Article ID | Journal | Published Year | Pages | File Type |
|---|---|---|---|---|
| 443252 | Journal of Molecular Graphics and Modelling | 2016 | 9 Pages |
•An MD model of a lipopolysaccharide was created as an extension to MARTINI.•The model was tested with MARTINI's polarized and non polarized water models.•Comparison was made with all-atom simulations as well as neutron scattering data.•The membrane structure was well reproduced by the coarse grained model.•A computational efficiency of 92× greater than all-atom simulations was achieved.
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.
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