Demonstrated convergence of the equilibrium ensemble for a fast united-residue protein model

@misc{citeulike:2694696, abstract = {Due to the time-scale limitations of all-atom simulation of proteins, there has been substantial interest in coarse-grained approaches. Some methods, like "Resolution Exchange," [E. Lyman et al., Phys. Rev. Lett. 96, 028105 (2006)] can accelerate canonical all-atom sampling, but require properly distributed coarse ensembles. We therefore demonstrate that full sampling can indeed be achieved in a sufficiently simplified protein model, as verified by a recently developed convergence analysis. The model accounts for protein backbone geometry in that rigid peptide planes rotate according to atomistically defined dihedral angles, but there are only two degrees of freedom (phi and psi dihedrals) per residue. Our convergence analysis indicates that small proteins (up to 89 residues in our tests) can be simulated for more than 50 "structural decorrelation times" in less than a week on a single processor. We show that the fluctuation behavior is reasonable, as well as discussing applications, limitations, and extensions of the model.}, author = {Ytreberg, Marty F. and Svetlana and Zuckerman, Daniel M. }, citeulike-article-id = {2694696}, eprint = {physics/0703222}, keywords = {coarse-grained, protein\_dynamics, struct\_decorr}, month = {Mar}, posted-at = {2008-04-21 10:13:08}, priority = {2}, title = {Demonstrated convergence of the equilibrium ensemble for a fast united-residue protein model}, url = {http://arxiv.org/abs/physics/0703222}, year = {2007} }

TY - ELEC ID - citeulike:2694696 L3 - citeulike-article-id:2694696 TI - Demonstrated convergence of the equilibrium ensemble for a fast united-residue protein model N2 - Due to the time-scale limitations of all-atom simulation of proteins, there has been substantial interest in coarse-grained approaches. Some methods, like "Resolution Exchange," [E. Lyman et al., Phys. Rev. Lett. 96, 028105 (2006)] can accelerate canonical all-atom sampling, but require properly distributed coarse ensembles. We therefore demonstrate that full sampling can indeed be achieved in a sufficiently simplified protein model, as verified by a recently developed convergence analysis. The model accounts for protein backbone geometry in that rigid peptide planes rotate according to atomistically defined dihedral angles, but there are only two degrees of freedom (phi and psi dihedrals) per residue. Our convergence analysis indicates that small proteins (up to 89 residues in our tests) can be simulated for more than 50 "structural decorrelation times" in less than a week on a single processor. We show that the fluctuation behavior is reasonable, as well as discussing applications, limitations, and extensions of the model. KW - coarse-grained KW - protein_dynamics KW - struct_decorr AU - Ytreberg, Marty AU - Svetlana AU - Zuckerman, Daniel PY - 2007/Mar/24/ UR - http://arxiv.org/abs/physics/0703222 ER -