The dominant reaction pathway (DRP) is an algorithm to microscopically compute the most probable reaction pathways in the overdamped Langevin dynamics without investing computational time in simulating the local thermal motion in the metastable configurations. In order to test the accuracy of such a method, we investigate the dynamics of the folding of a β hairpin within a model that accounts for both native and non-native interactions. We compare the most probable folding pathways calculated with the DRP method with the folding trajectories obtained directly from molecular dynamics simulations. We find that the two approaches give consistent results.
Faccioli, P., Lonardi, A., Orland, H. (2010). Dominant reaction pathways in protein folding: A direct validation against molecular dynamics simulations. THE JOURNAL OF CHEMICAL PHYSICS, 133(4) [10.1063/1.3459097].
Dominant reaction pathways in protein folding: A direct validation against molecular dynamics simulations
Faccioli, P
;
2010
Abstract
The dominant reaction pathway (DRP) is an algorithm to microscopically compute the most probable reaction pathways in the overdamped Langevin dynamics without investing computational time in simulating the local thermal motion in the metastable configurations. In order to test the accuracy of such a method, we investigate the dynamics of the folding of a β hairpin within a model that accounts for both native and non-native interactions. We compare the most probable folding pathways calculated with the DRP method with the folding trajectories obtained directly from molecular dynamics simulations. We find that the two approaches give consistent results.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.