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Principal component analysis of lipid molecule conformational changes in molecular dynamics simulations

Pavel Buslaev 1 Valentin I. Gordeliy 1, 2, 3 Sergei Grudinin 1, 4, * Ivan Yu. Gushchin 1, 2 
* Corresponding author
4 NANO-D - Algorithms for Modeling and Simulation of Nanosystems
Inria Grenoble - Rhône-Alpes, Grenoble INP - Institut polytechnique de Grenoble - Grenoble Institute of Technology, LJK - Laboratoire Jean Kuntzmann
Abstract : Molecular dynamics simulations of lipid bilayers are ubiquitous nowadays. Usually, either global properties of the bilayer or some particular characteristics of each lipid molecule are evaluated in such simulations, but the structural properties of the molecules as a whole are rarely studied. Here, we show how a comprehensive quantitative description of conformational space and dynamics of a single lipid molecule can be achieved via the principal component analysis (PCA). We illustrate the approach by analyzing and comparing simulations of DOPC bilayers obtained using eight different force fields: all-atom generalized AMBER, CHARMM27, CHARMM36, Lipid14 and Slipids, and united-atom Berger, GROMOS43A1-S3 and GROMOS54A7. Similarly to proteins, most of the structural variance of a lipid molecule can be described by only a few principal components. These major components are similar in different simulations, although there are notable distinctions between the older and newer force fields, and between the all-atom and united-atom force fields. The DOPC molecules in the simulations generally equilibrate on the timescales of tens to hundreds of nanoseconds. The equilibration is the slowest in the GAFF simulation, and the fastest in the Slipids simulation. Somewhat unexpectedly, the equilibration in the united-atom force fields is generally slower than in the all-atom force fields. Overall, there is a clear separation between the more variable previous generation force fields, and significantly more similar new generation force fields (CHARMM36, Lipid14, Slipids). We expect that the presented approaches will be useful for quantitative analysis of conformations and dynamics of individual lipid molecules in other simulations of lipid bilayers.
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Submitted on : Monday, January 18, 2016 - 5:03:52 PM
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Pavel Buslaev, Valentin I. Gordeliy, Sergei Grudinin, Ivan Yu. Gushchin. Principal component analysis of lipid molecule conformational changes in molecular dynamics simulations. Journal of Chemical Theory and Computation, 2016, 12 (3), pp.1019-1028. ⟨10.1021/acs.jctc.5b01106⟩. ⟨hal-01258167⟩



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