Abstract
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.
Original language | English (US) |
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Pages (from-to) | 1136-1141 |
Number of pages | 6 |
Journal | Journal of Computational Chemistry |
Volume | 27 |
Issue number | 11 |
DOIs | |
State | Published - Aug 2006 |
Keywords
- Alanine dipeptide
- CHARMM
- Conformational transition
- Dynamic importance sampling
- Multiple pathways
ASJC Scopus subject areas
- General Chemistry
- Computational Mathematics