Automatic detection of hidden dimensions to obtain appropriate reaction coordinates in the Outlier FLOODing (OFLOOD) method
Abstract
As a strategy for reproducing rare, biologically important events, we previously developed the Outlier FLOODing (OFLOOD) method [J. Comput. Chem. 36 (2015) 97-102]. This method utilizes conformational resampling from rarely occurring states, detected as outliers, to promote conformational transitions relevant to the rare events. However, to perform OFLOOD efficiently requires specifying a set of appropriate reaction coordinates (RCs) with non-trivial specifications. Therefore, in this paper, we propose a strategy to obtain a set of appropriate RCs using a method where the best set of RCs are automatically searched from the initially given RCs, via clustering the states of biomolecules.
- Publication:
-
Chemical Physics Letters
- Pub Date:
- October 2015
- DOI:
- 10.1016/j.cplett.2015.09.031
- Bibcode:
- 2015CPL...639..269H