8 research outputs found
Kinetic Analysis of Discrete Path Sampling Stationary Point Databases
Analysing stationary point databases to extract phenomenological rate
constants can become time-consuming for systems with large potential energy
barriers. In the present contribution we analyse several different approaches
to this problem. First, we show how the original rate constant prescription
within the discrete path sampling approach can be rewritten in terms of
committor probabilities. Two alternative formulations are then derived in which
the steady-state assumption for intervening minima is removed, providing both a
more accurate kinetic analysis, and a measure of whether a two-state
description is appropriate. The first approach involves running additional
short kinetic Monte Carlo (KMC) trajectories, which are used to calculate
waiting times. Here we introduce `leapfrog' moves to second-neighbour minima,
which prevent the KMC trajectory oscillating between structures separated by
low barriers. In the second approach we successively remove minima from the
intervening set, renormalising the branching probabilities and waiting times to
preserve the mean first-passage times of interest. Regrouping the local minima
appropriately is also shown to speed up the kinetic analysis dramatically at
low temperatures. Applications are described where rates are extracted for
databases containing tens of thousands of stationary points, with effective
barriers that are several hundred times kT.Comment: 28 pages, 1 figure, 4 table
A Doubly Nudged Elastic Band Method for Finding Transition States
A modification of the nudged elastic band (NEB) method is presented that
enables stable optimisations to be run using both the limited-memory
quasi-Newton (L-BFGS) and slow-response quenched velocity Verlet (SQVV)
minimisers. The performance of this new `doubly nudged' DNEB method is analysed
in conjunction with both minimisers and compared with previous NEB
formulations. We find that the fastest DNEB approach (DNEB/L-BFGS) can be
quicker by up to two orders of magnitude. Applications to permutational
rearrangements of the seven-atom Lennard-Jones cluster (LJ7) and highly
cooperative rearrangements of LJ38 and LJ75 are presented. We also outline an
updated algorithm for constructing complicated multi-step pathways using
successive DNEB runs.Comment: 13 pages, 8 figures, 2 table
Correlated ab Initio Study of Nucleic Acid Bases and Their Tautomers in the Gas Phase, in a Microhydrated Environment and in Aqueous Solution. Guanine: Surprising Stabilization of Rare Tautomers in Aqueous Solution
Finding pathways between distant local minima
We report a new algorithm for constructing pathways between local minima that
involve a large number of intervening transition states on the potential energy
surface. A significant improvement in efficiency has been achieved by changing
the strategy for choosing successive pairs of local minima that serve as
endpoints for the next search. We employ Dijkstra's algorithm to identify the
`shortest' path corresponding to missing connections within an evolving
database of local minima and the transition states that connect them. The
metric employed to determine the shortest missing connection is a function of
the minimised Euclidean distance. We present applications to the formation of
buckminsterfullerene and to the folding of the B1 domain of protein G,
tryptophan zippers, and the villin headpiece subdomain. The corresponding
pathways contain up to 163 transition states, and will be used in future
discrete path sampling calculations.Comment: 29 pages, 4 figure