Comparing Solvent Models for Molecular Dynamics of Protein
نویسندگان
چکیده
Discrete nature of water plays critical role in protein folding and thermodynamics. Explicit all-atom modeling of solvent severely limits the length and time scales of molecular dynamics simulations of protein. In this project, we evaluated accuracy and computational efficiency of four different solvent models, all-atom solvent models ( SPC/E and TIP3P ), Generalized Born Implicit Solvent, and CoarseGrained solvent model. CG force-field, for solvent interactions, is determined using Force-matching with exclusion technique. Explicit and implicit solvent simulations are compared with vacuum to study the effects of solvent on protein structure.
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