Multiple state transition interface sampling of alanine dipeptide in explicit solvent.
We have applied the recently developed multiple state transition interface sampling approach to alanine dipeptide in explicit water. We extract the rate constant matrix for configurational changes between each pair of metastable states. The results are comparable with values from previous literature and show that the method is applicable to biomolecular systems.
Van't Hoff Institute for Molecular Sciences, University of Amsterdam, PO Box 94157, 1090 GD Amsterdam, The Netherlands.
Wei-Na
WN
Du
Kristen A
KA
Marino
Peter G
PG
Bolhuis
D003198:Computer Simulation; D004151:Dipeptides / Q000737:chemistry*; D008958:Models, Molecular; D008968:Molecular Conformation; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
D004151:Dipeptides; D014867:Water; C002956:alanylalanine