Multiple state transition path sampling
- 10 December 2008
- journal article
- research article
- Published by AIP Publishing in The Journal of Chemical Physics
- Vol. 129 (22) , 224107
- https://doi.org/10.1063/1.3029696
Abstract
We developed a multiple state transition path sampling (TPS) approach in which it is possible to simultaneously sample pathways connecting a number of different stable states. Based on the original formulation of the TPS we have extended the path ensemble to include trajectories connecting not only two distinct stable states but any two states defined within a system. The multiple state TPS approach is useful in complex systems exhibiting a number of intermediate stable states that are interconnected in phase space. Combining this approach with transition interface sampling we can also directly obtain an expression for the rate constants of all possible transitions within the system.Keywords
This publication has 19 references indexed in Scilit:
- Hierarchical analysis of conformational dynamics in biomolecules: Transition networks of metastable statesThe Journal of Chemical Physics, 2007
- Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamicsThe Journal of Chemical Physics, 2007
- Long‐Time Protein Folding Dynamics from Short‐Time Molecular Dynamics SimulationsMultiscale Modeling & Simulation, 2006
- Interplay between Structure and Size in a Critical Crystal NucleusPhysical Review Letters, 2005
- Elaborating transition interface sampling methodsPublished by Elsevier ,2004
- Escaping free-energy minimaProceedings of the National Academy of Sciences, 2002
- Transition Path SamplingAdvances in Chemical Physics, 2002
- A method for accelerating the molecular dynamics simulation of infrequent eventsThe Journal of Chemical Physics, 1997
- Constrained reaction coordinate dynamics for the simulation of rare eventsChemical Physics Letters, 1989
- Monte Carlo free energy estimates using non-Boltzmann sampling: Application to the sub-critical Lennard-Jones fluidChemical Physics Letters, 1974