A hidden Markov state model has been applied to classical molecular dynamics simulated small peptide in explicit water. The methodology allows increasing the time resolution of the model and describe the dynamics with the precision of 0.3 ps (comparing to 6 ps for the standard methodology). It also permits the investigation of the mechanisms of transitions between the conformational states of the peptide. The detailed description of one of such transitions for the studied molecule is presented.
|Number of pages||6|
|Journal||Journal of Molecular Liquids|
|Early online date||7 Jul 2012|
|Publication status||Published - Dec 2012|
- conformational transitions
- Markov state model
- protein dynamics