文档介绍：Biophysical Chemistry G4170:
Introduction to Molecular Dynamics
Ruhong Zhou
IBM Thomas Watson Research Center
Yorktown Heights, NY 10598
. SolvationSolvation ModelsModels
SolvationSolvation ModelsModels
ExplicitExplicit solventsolvent modelsmodels
Fixed charge models: SPC, SPC/E, TIP3P, TIP4P,
TIP5P, ST2,…
Polarizable water models: TIP4P/FQ, POL5,
MCDHO,…
ImplicitImplicit SolventSolvent modelsmodels
Poisson-Boltzman solver (Delphi, Honig)
Generalized Born Model (Still)
Karplus’ EEF1 model
Benoit Roux’s Spherical Solvent Boundary Potential
(SSBP)
ExplicitExplicit WaterWater ModelsModels Needed:Needed:
DewettingDewetting TransitionTransition
BphC Enzyme
R Zhou, X Huang, C Margulius, B Berne, Science 305, 1605, 2004
ExplicitExplicit WaterWater modelsmodels
SPC,SPC, SPC/E,SPC/E, TIPnP,TIPnP, POL5POL5
WaterWater ModelModel GeometriesGeometries
WaterWater ModelModel ParametersParameters
• SPC, SPC/E (Berendsen)
• TIP3P, TIP4P, TIP5P (Jorgensen)
• TIP4P/FQ, POL5 (Berne)
PropertiesProperties ofof WaterWater ModelsModels
WaterWater densitydensity maximummaximum
WaterWater parison
M. Mahoney and W. L. Jorgensen, J. Chem. Phys. 112, 8910, 2000