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Strongly coarse-grained membrane simulations



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Strongly coarse grained membrane simulations Markus Deserno Carnegie Mellon University Department of Physics with many thanks to Ira Cooke Benedict Reynwar Gregoria Illya Vagelis Harmandaris Kurt Kremer and our afternoon experts Mingyang Hu and Patrick Diggins International Workshop on Coarse Grained Biomolecula Modeling October 17 21 2011 Lausanne Switzerland October 19 2011 Why coarse graining If you haven t figured that out by now you should ask for your money back No seriously Why coarse graining Why coarse graining Efficiency Insight Efficiency Does that mean just bigger systems No Not just Efficiency Lindahl E Edholm O Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations Biophys J 79 426 433 2000 All atom lipid bilayer 20nm 20nm 1024 lipids 10ns What if we want a boxlength of L 200nm How does computing effort scale with L effort 2 L 4 L 6 L Amount of material Equilibration time Efficiency 20nm 200nm Million times more computationally expensive 20 doublings of computer power 20 x 2 years Moore s law 40 years I ll be retired by then best case scenario Efficiency Stated differently The amount of material scales with the membrane area A Using a domain decomposition scheme this can in the best case be compensated by increasing the number of processors proportional to A But the simulation time towards equilibration scales like A3 This still leaves an uncompensated factor of A2 that you must do more work or have faster chips or better ideas Efficiency Coarse graining cannot just help you to look at much bigger systems It can help you to get well equilibrated data for somewhat bigger systems If someone offers you 1000 times more computational power you should make your membrane length 3 times bigger and simulate it for 100 time longer Efficiency Coarse graining cannot just help you to look at much bigger systems It can help you to get well equilibrated data for somewhat bigger systems Unfortunately the latter doesn t



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