Oct 24, 2007

Selective sampling of transition paths

The Journal of Chemical Physics
Xuebing FuYi Qin Gao

Abstract

In this short paper, we introduce an approximate method for the quick estimate of rate constants based on a simple sampling method of reactive transition paths over high energy barriers. It makes use of the previously introduced accelerated molecular dynamics (MD) simulation method to generate initial points for trajectory shooting. The accelerated MD simulations, although with the loss of real dynamics, lead to a quick calculation of thermodynamic properties and at the same time produce an ensemble of configurations with an enhanced sampling over the phase space that is more "reactive." The forward/backward trajectory shooting as that used in the transition path sampling method is then initiated from the configurations obtained from accelerated MD simulations to generate transition paths on the original unbiased potential. This method selectively enhances sampling of successful trajectories and at the same time accelerates significantly the calculation of rate constants.

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  • Citations9

References

Mentioned in this Paper

High Molecular Weight Kininogen Deficiency
Sampling Method
Molecular Dynamics
Sampling Design

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