David Aristoff, Tony Lelièvre, Christopher G. Mayne, and Ivan Teo.
Adaptive multilevel splitting in molecular dynamics simulations.
ESAIM: Proceedings and Surveys, 48:215-225, 2015.
(PMC: PMC4440697)
ARIS2015-CM
Adaptive Multilevel Splitting (AMS) is a replica-based rare event sampling
method that has
been used successfully in high-dimensional stochastic simulations to
identify trajectories
across a high potential barrier separating one metastable state from
another, and to
estimate the probability of observing such a trajectory. An attractive
feature of AMS is that,
in the limit of a large number of replicas, it remains valid regardless of the
choice of
reaction coordinate used to characterize the trajectories. Previous
studies have shown AMS
to be accurate in Monte Carlo simulations. In this study, we extend the
application of AMS
to molecular dynamics simulations and demonstrate its effectiveness
using a simple test
system. Our conclusion paves the way for useful applications, such as
molecular dynamics
calculations of the characteristic time of drug dissociation from a protein
target.
Download Full Text
The manuscripts available on our site are provided for your personal
use only and may not be retransmitted or redistributed without written
permissions from the paper's publisher and author. You may not upload any
of this site's material to any public server, on-line service, network, or
bulletin board without prior written permission from the publisher and
author. You may not make copies for any commercial purpose. Reproduction
or storage of materials retrieved from this web site is subject to the
U.S. Copyright Act of 1976, Title 17 U.S.C.
