Paper Citing NAMD - Abstract
Mullen, Ryan Gotchy; Shea, Joan-Emma; Peters, Baron
Transmission Coefficients, Committors, and Solvent Coordinates in Ion-Pair Dissociation
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:659-667, FEB 2014
From a hypothetical perfect dividing surface, all trajectories commit to opposite basins in forward and backward time without recrossing, transition state theory is exact, the transmission coefficient is one, and the committor distribution is perfectly focused at 1/2. However, chemical reactions in solution and other real systems often have dynamical trajectories that recross the dividing surface. To separate true dynamical effects from effects of a nonoptimal dividing surface, the dividing surface and/or reaction coordinate should be optimized before computing transmission coefficients. For NaCl dissociation in TIP3P water, we show that recrossing persists even when the 1/2-committor surface itself is used as the dividing surface, providing evidence that recrossing cannot be fully eliminated from the dynamics for any configurational coordinate. Consistent with this finding, inertial likelihood maximization finds a combination of ion-pair distance and two solvent coordinates that improves the committor distribution and increases the transmission coefficient relative to those for ion-pair distance alone, but recrossing is not entirely eliminated. Free energy surfaces for the coordinates identified by inertial likelihood maximization show that the intrinsic recrossing stems from anharmonicity and shallow intermediates that remain after dimensionality reduction to the dynamically important variables.
