Spring shooting – A module for improving efficiency of transition path sampling


Transition path sampling is most efficient when paths are generated from the top of the free energy barrier. However, complex (biomolecular) activated processes, such as nucleation or protein binding/unbinding, can have asymmetric and peaked barriers. Using uniform selection on these type of processes will not be efficient, as it, on average, results in selected points that are not on the top of the barrier. Paths generated from these points have a low acceptance probability and accepted transition paths decorrelate slowly, resulting in a low overall efficiency. The Spring shooting module was developed to increase the efficiency of path sampling of these types of barriers, without any prior knowledge of the barrier shape. The spring shooting algorithm uses a shooting point selector that is biased with a spring potential. This bias pulls the selection of points towards the transition state at the top of the barrier. The paths that are generated from points selected by this biased selector therefore have an increased acceptance probability and the decorrelation between accepted transition paths is also increased. This results in a higher overall efficiency. The spring shooting algorithm is described in more detail in a paper by Brotzakis and Bolhuis. [1]  This module was developed during the ESDW on classical molecular dynamics held in Amsterdam.


[1] Z. F. Brotzakis, P. G. Bolhuis A one-way shooting algorithm for transition path sampling of asymmetric barriers J. Chem. Phys. 145 (2016) 164112