Paper Citing NAMD - Abstract
Peters, Baron; Beckham, Gregg T.; Trout, Bernhardt L.
Extensions to the likelihood maximization approach for finding reaction coordinates
JOURNAL OF CHEMICAL PHYSICS, 127 Art. No. 034109, JUL 21 2007
This paper extends our previous work on obtaining reaction coordinates from aimless shooting and likelihood maximization. We introduce a simplified version of aimless shooting and a half-trajectory likelihood score based on the committor probability. Additionally, we analyze and compare the absolute log-likelihood score for perfect and approximate reaction coordinates. We also compare the aimless shooting and likelihood maximization approach to the earlier genetic neural network (GNN) approach of Ma and Dinner [J. Phys. Chem. B 109, 6769 (2005)]. For a fixed number of total trajectories in the GNN approach, the accuracy of the transition state ensemble decreases as the number of trajectories per committor probability estimate increases. This quantitatively demonstrates the benefit of individual committor probability realizations over committor probability estimates. Furthermore, when the least squares score of the GNN approach is applied to individual committor probability realizations, the likelihood score still provides a better approximation to the true transition state surface. Finally, the polymorph transition in terephthalic acid demonstrates that the new half-trajectory likelihood scheme estimates the transition state location more accurately than likelihood schemes based on the probability of being on a transition path. (C) 2007 American Institute of Physics.
