Journal
JOURNAL OF CHEMICAL PHYSICS
Volume 130, Issue 22, Pages -Publisher
AMER INST PHYSICS
DOI: 10.1063/1.3147465
Keywords
-
Funding
- National Science Foundation [0553719]
- ACSPRF grant
- Div Of Chem, Bioeng, Env, & Transp Sys
- Directorate For Engineering [0553719] Funding Source: National Science Foundation
Ask authors/readers for more resources
Forward flux sampling (FFS) simulations were used to study the kinetics of alanine dipeptide both in vacuum and in explicit solvent. The recently proposed FFS least-squares estimation approach and an algorithm that optimizes the position of the interfaces were implemented to determine a reaction coordinate that adequately describes the transition dynamics. A new method is also introduced to try to ensure that the ensemble of starting points (for the trial trajectories) is properly sampled. The rate constant estimates for the C7(eq) double right arrow C5 transition of alanine dipeptide in vacuum were used to demonstrate the consistency between Monte Carlo and molecular dynamics (MD) simulations. FFS-MD simulations were then performed for the study of the beta(2)/alpha(R) double right arrow C5/C7(eq) transition in explicit solvent. The kinetic results for both systems in vacuum and explicit solvent are in general agreement with previous experimental and computational studies for this peptide. In vacuum, an additional dihedral angle besides the one typically used as order parameter is identified as a significant variable in the reaction coordinate model. In solution, several dihedral angles and variables that describe the solvent action on the molecule's dynamics are found to play a significant role in the description of the system's dynamics. (C) 2009 American Institute of Physics. [DOI: 10.1063/1.3147465]
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available