Finding pathways between distant local minima

Details Finding pathways between distant local minima Finding pathways between distant local minima

2005-04-29

arxiv.org/abs/cond-mat/0504785v1

Physics

Condensed Matter

Other Condensed Matter

29 pages, 4 figures

Scientific paper

10.1063/1.1931587

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.

Affiliated with

Also associated with

No associations

Rating

Finding pathways between distant local minima does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.

If you have personal experience with Finding pathways between distant local minima, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Finding pathways between distant local minima will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFWR-SCP-O-402050