Abstract
A multiscale modeling approach is applied for simulations of lipids and lipid assemblies on mesoscale. First, molecular dynamics simulation of initially disordered system of lipid molecules in water within all-atomic model was carried out. On the next stage, structural data obtained from the molecular dynamics (MD) simulation were used to build a coarse-grained (ten sites) lipid model, with effective interaction potentials computed by the inverse Monte Carlo method. Finally, several simulations of the coarse-grained model on longer length- and time-scale were performed, both within Monte Carlo and molecular dynamics simulations: a periodical sample of lipid molecules ordered in bilayer, a free sheet of such bilayer without periodic boundary conditions, formation of vesicle from a plain membrane, process of self-assembly of lipids randomly dispersed in volume. It was shown that the coarse-grained model, developed exclusively from all-atomic simulation data, reproduces well all the basic features of lipids in water solution.
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Acknowledgements
The author thanks the Center for Parallel Computing (PDC) at the Royal Institute of Technology for granting the use of computer facilities. The work has been supported by the Swedish Research Council (Vetenskapsrådet)
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Lyubartsev, A.P. Multiscale modeling of lipids and lipid bilayers. Eur Biophys J 35, 53–61 (2005). https://doi.org/10.1007/s00249-005-0005-y
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DOI: https://doi.org/10.1007/s00249-005-0005-y