Free Energy and Kinetics of Conformational Transitions from Voronoi Tessellated Milestoning with Restraining Potentials Export

@article{citeulike:6045577, abstract = {Milestoning is a method aimed at reconstructing the statistical properties of the long-time dynamics of a system by exploiting the crossing statistics of a set of hypersurfaces, called the ” milestones”, placed along the reaction coordinate [Faradjian and Elber, J. Chem. Phys. 2004, 120, 10880]. Recently, Vanden-Eijnden and Venturoli [J. Chem. Phys. 2009, 130, 194101] showed that when a complete Voronoi tessellation of the configurational space is available, milestoning can be reformulated to utilize the statistics from a series of independent simulations, each confined within a single cell via strict reflections at the boundaries. As a byproduct, this ” Voronoi tessellated milestoning” method also permits to compute the free energy of the tessellation. Here, the method is extended to support the usage of differentiable restraining potentials to confine the trajectories within each cell.}, author = {Maragliano, Luca and Vanden-Eijnden, Eric and Roux, Benoît}, citeulike-article-id = {6045577}, citeulike-linkout-0 = {http://dx.doi.org/10.1021/ct900279z}, citeulike-linkout-1 = {http://pubs.acs.org/doi/abs/10.1021/ct900279z}, day = {13}, doi = {10.1021/ct900279z}, journal = {Journal of Chemical Theory and Computation}, keywords = {conformational\_flexibility, energylandscape, free, freeenergy, kinetics, network}, month = {October}, number = {10}, pages = {2589--2594}, posted-at = {2009-10-31 04:32:06}, priority = {2}, title = {Free Energy and Kinetics of Conformational Transitions from Voronoi Tessellated Milestoning with Restraining Potentials}, url = {http://dx.doi.org/10.1021/ct900279z}, volume = {5}, year = {2009} }

TY - JOUR ID - citeulike:6045577 L3 - citeulike-article-id:6045577 N2 - Milestoning is a method aimed at reconstructing the statistical properties of the long-time dynamics of a system by exploiting the crossing statistics of a set of hypersurfaces, called the “milestones”, placed along the reaction coordinate [Faradjian and Elber, J. Chem. Phys. 2004, 120, 10880]. Recently, Vanden-Eijnden and Venturoli [J. Chem. Phys. 2009, 130, 194101] showed that when a complete Voronoi tessellation of the configurational space is available, milestoning can be reformulated to utilize the statistics from a series of independent simulations, each confined within a single cell via strict reflections at the boundaries. As a byproduct, this “Voronoi tessellated milestoning” method also permits to compute the free energy of the tessellation. Here, the method is extended to support the usage of differentiable restraining potentials to confine the trajectories within each cell. IS - 10 JF - Journal of Chemical Theory and Computation EP - 2594 TI - Free Energy and Kinetics of Conformational Transitions from Voronoi Tessellated Milestoning with Restraining Potentials VL - 5 SP - 2589 KW - conformational_flexibility KW - energylandscape KW - free KW - freeenergy KW - kinetics KW - network AU - Maragliano, Luca AU - Vanden-Eijnden, Eric AU - Roux, Benoît PY - 2009/10/13/ UR - http://dx.doi.org/10.1021/ct900279z ER -