A fast method for calculating geometry-dependent net atomic charges for polypeptides

Article Abstract:

A novel method for calculating geometry-dependent atomic charges (GDACs) for polypeptides, which overcomes several limitations of partial equalization, is presented. The GDAC method provides a simple and direct approach for calculating molecular charge distributions in proteins.

Chemical properties, Atomic properties

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Molecular dynamics with the united-residue model of polypeptide chains. I. Lagrange equations of motion and tests of numerical stability in the microcanonical mode

Article Abstract:

The equations of motion for the physics-based united-residue (UNRES) force field are derived by implementing the Lagrange formalism. The results suggest that the effective time unit in UNRES dynamics is much larger than that of all-atom dynamics.

Analysis, Usage, Molecular dynamics, Lagrange equations, Structure

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Derivation of a new force field for crystal-structure prediction using global optimization: nonbonded potential parameters for amines, imidazoles, amides, and carboxylic acids

Article Abstract:

New nonbonded parameters of all-atom force field are presented for amines, imidazoles, amides, and carboxylic acids. A general force field for the prediction of crystal and protein structures is derived from the results.

Methods, Crystal structure, Protein structure, Mathematical optimization, Optimization theory

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