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Atomistic vs. Coarse Grained Simulations

Atomistic vs. Coarse Grained Simulations. all atoms vs. four-to-one mapping long range vs. short range interactions only quantitative vs. semi-quantitative slow (ns) vs. fast (ms). 1 coarse grained water 4 atomistic water. =.

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Atomistic vs. Coarse Grained Simulations

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  1. Atomistic vs. Coarse Grained Simulations all atoms vs. four-to-one mapping long range vs. short range interactions only quantitative vs. semi-quantitative slow (ns) vs. fast (ms) 1 coarse grained water 4 atomistic water = atomistic coarse grained

  2. Aggregation into a DPPC bilayer – coarse grained model composition: 1600 DPPC 250000 H2O 0 ns 5 ns 1 ns cell size: 20x20x20 nm simulation time: 250 ns 15 ns 50 ns 100 ns 150 ns 180 ns 250 ns

  3. Aggregation of DPPC into vesicles composition: 1600 DPPC 1000000 H2O simulation time: 100 ns cell size: 30x30x30 nm Surrounding water starting structure (t=0 ns)

  4. 0 ns random 5 ns worms 10 ns bicelle 20 ns bicelle 60 ns cup 80 ns vesicle

  5. LAMELLAR STALK HEMIFUSION FUSION PORE RHOMBIC HEXAGONAL CUBIC

  6. Lamellar to Hexagonal Transition for DOPE at low hydration in agreement with experiment (Rand etal) t = 0ns t = 20 ns t = 100 ns T=280 -> 320K stalk formation hexagonal phase

  7. t = 20 ns t = 100 ns stalk formation hexagonal phase

  8. Folding Transition States in Proteins In collaboration with the group of Chris Dobson in Cambridge we have looked at transition states in the folding of SH3 domains. Objective: To evaluate the folding propensity of proposed transition states (TS) of the a-spectrin SH3 domain using molecular dynamics (MD) simulations with an explicit representation of the solvent. Some of the proposed transition states fold other do not.

  9. Examples showing the native state, a proposed transition state and results of 2 independent folding simulations. Configuration 2 Native Init Folding unsuccessful run 1 run 2 Configuration 4 Configuration 3 Folding successful

  10. Status of our contribution: • Trajectories of the simulations mentioned above can be made available on request • While we have not appointed anyone specifically on the project we are in the • process of advertising. • Our aim is to specifically appoint a person focusing on code development who • could interact with those groups involved in methods development and exploit • our preexisting simulations..

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