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Main chain torsions of alanine dipeptide are parameterized into coupled 2-dimensional Fourier expansions based on quantum mechanical (QM) calculations at M06 2X/aug-cc-pvtz//HF/6-31G** level. Solvation effect is considered by employing polarizable continuum model. Utilization of the M06 2X functional leads to precise potential energy surface that is(More)
Papers published in Hydrology and Earth System Sciences Discussions are under open-access review for the journal Hydrology and Earth System Sciences Abstract The representative elementary watershed (REW) approach proposed by Reggiani et al. (1998, 1999) represents an attempt to develop a scale adaptable modeling framework for the hydrological research(More)
A newly developed AMBER compatible force ¯eld with coupled backbone torsion potential terms (AMBER03 2D) is utilized in a folding simulation of a mini-protein Trp-cage. Through replica exchange and direct molecular dynamics (MD) simulations, a multi-step folding mechanism with a synergetic folding of the hydrophobic core (HPC) and the-helix in the ¯nal(More)
A new modification to the AMBER force field that incorporates the coupled two-dimensional main chain torsion energy has been evaluated for the balanced representation of secondary structures. In this modified AMBER force field (AMBER03(2D)), the main chain torsion energy is represented by 2-dimensional Fourier expansions with parameters fitted to the(More)
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