Peptide Folding Kinetics from Replica Exchange Molecular Dynamics Export

@misc{citeulike:2500773, abstract = {We show how accurate kinetic information, such as the rates of protein folding and unfolding, can be extracted from replica-exchange molecular dynamics (REMD) simulations. From the brief and continuous trajectory segments between replica exchanges, we estimate short-time propagators in conformation space and use them to construct a master equation. For a helical peptide in explicit water, we determine the rates of transitions both locally between microscopic conformational states and globally for folding and unfolding. We show that accurate rates in the \~{}1/(100 ns) to \~{}1/(1 ns) range can be obtained from REMD with exchange times of 5 ps, in excellent agreement with results from long equilibrium molecular dynamics.}, archivePrefix = {arXiv}, author = {Buchete, Nicolae-Viorel and Hummer, Gerhard}, citeulike-article-id = {2500773}, citeulike-linkout-0 = {http://arxiv.org/abs/0710.5533}, citeulike-linkout-1 = {http://arxiv.org/pdf/0710.5533}, day = {11}, eprint = {0710.5533}, keywords = {folding, kinetics, master\_equation}, month = {Feb}, posted-at = {2008-03-10 13:30:51}, priority = {2}, title = {Peptide Folding Kinetics from Replica Exchange Molecular Dynamics}, url = {http://arxiv.org/abs/0710.5533}, year = {2008} }

TY - ELEC ID - citeulike:2500773 L3 - citeulike-article-id:2500773 N2 - We show how accurate kinetic information, such as the rates of protein folding and unfolding, can be extracted from replica-exchange molecular dynamics (REMD) simulations. From the brief and continuous trajectory segments between replica exchanges, we estimate short-time propagators in conformation space and use them to construct a master equation. For a helical peptide in explicit water, we determine the rates of transitions both locally between microscopic conformational states and globally for folding and unfolding. We show that accurate rates in the ~1/(100 ns) to ~1/(1 ns) range can be obtained from REMD with exchange times of 5 ps, in excellent agreement with results from long equilibrium molecular dynamics. TI - Peptide Folding Kinetics from Replica Exchange Molecular Dynamics KW - folding KW - kinetics KW - master_equation AU - Buchete, Nicolae-Viorel AU - Hummer, Gerhard PY - 2008/Feb/11/ UR - http://arxiv.org/abs/0710.5533 ER -