Multiple pathways in conformational transitions of the alanine dipeptide: an application of dynamic importance sampling.
We present multiple dynamic transition pathways on the two-dimensional dihedral plane between conformational states of the alanine dipeptide. The method used in this study is dynamic importance sampling (DIMS). To perform DIMS, unbiased molecular dynamic simulations are used to generate equilibrium ensembles for the alanine dipeptide within different states. Free energy surfaces on the dihedral plane are calculated from the equilibrium simulations, and four energy minima defined from the surface are used as the starting and ending points for DIMS dynamics. The DIMS method represents an important step towards finding multiple transition pathways within complex biomolecular systems.
Jang
Hyunbum
H
Department of Physiology, Johns Hopkins University, Baltimore, Maryland 21205, USA. jangh@ncifcrf.gov
Woolf
Thomas B
TB
D000409:Alanine / Q000737:chemistry*; D003198:Computer Simulation; D004151:Dipeptides / Q000737:chemistry*; D008968:Molecular Conformation; D011336:Probability
D004151:Dipeptides; C002956:alanylalanine; D000409:Alanine