Free-Energy Landscape for β Hairpin Folding from Combined Parallel Tempering and Metadynamics Export

@article{citeulike:3888201, abstract = {doi: 10.1021/ja062463w We develope a new free-energy method, based on the combination of parallel tempering and metadynamics, and apply this method to the calculation of the free-energy landscape of the folding beta hairpin in explicit water. We show that the combined method greatly improves the performance of both parallel tempering and metadynamics. In particular, we are able to sample the high free-energy regions, which are not accessible with conventional parallel tempering. We use our results to calculate the difference in entropy and enthalpy between the folded and the unfolded state and to characterize the most populated configurations in the relevant free-energy basins.}, author = {Bussi, Giovanni and Gervasio, Francesco L. and Laio, Alessandro and Parrinello, Michele}, citeulike-article-id = {3888201}, citeulike-linkout-0 = {http://dx.doi.org/10.1021/ja062463w}, citeulike-linkout-1 = {http://pubs.acs.org/doi/abs/10.1021/ja062463w}, day = {1}, doi = {10.1021/ja062463w}, journal = {Journal of the American Chemical Society}, keywords = {folding, metadynamics, molecular\_dynamics}, month = {October}, number = {41}, pages = {13435--13441}, posted-at = {2009-01-15 10:54:09}, priority = {2}, title = {Free-Energy Landscape for β Hairpin Folding from Combined Parallel Tempering and Metadynamics}, url = {http://dx.doi.org/10.1021/ja062463w}, volume = {128}, year = {2006} }

TY - JOUR ID - citeulike:3888201 L3 - citeulike-article-id:3888201 N2 - doi: 10.1021/ja062463w We develope a new free-energy method, based on the combination of parallel tempering and metadynamics, and apply this method to the calculation of the free-energy landscape of the folding beta hairpin in explicit water. We show that the combined method greatly improves the performance of both parallel tempering and metadynamics. In particular, we are able to sample the high free-energy regions, which are not accessible with conventional parallel tempering. We use our results to calculate the difference in entropy and enthalpy between the folded and the unfolded state and to characterize the most populated configurations in the relevant free-energy basins. IS - 41 JF - Journal of the American Chemical Society EP - 13441 TI - Free-Energy Landscape for β Hairpin Folding from Combined Parallel Tempering and Metadynamics VL - 128 SP - 13435 KW - folding KW - metadynamics KW - molecular_dynamics AU - Bussi, Giovanni AU - Gervasio, Francesco AU - Laio, Alessandro AU - Parrinello, Michele PY - 2006/10/01/ UR - http://dx.doi.org/10.1021/ja062463w ER -