Presentation on theme: "Atomistic vs. Coarse Grained Simulations all atoms vs. four-to-one mapping long range vs. short range interactions only quantitative vs. semi-quantitative."— Presentation transcript:
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
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
t = 20 ns t = 100 ns stalk formation hexagonal phase
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.
Init Native run 1 Configuration 3 Configuration 4 run 2 Configuration 2 Examples showing the native state, a proposed transition state and results of 2 independent folding simulations. Folding successful Folding unsuccessful
Status of our contribution: 1.Trajectories of the simulations mentioned above can be made available on request 2.While we have not appointed anyone specifically on the project we are in the process of advertising. 3.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..