Molecular Dynamics of Small Peptides Using Ergodic Trajectories
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A comparative study of the molecular dynamics of natural amino acid residues and some of their homologs and isomers is carried out. MD protocols not interfering with a principle of equidistribution of energy on degrees of freedom are used. Poincare cross-sections are considered. Dynamic properties of conformational degrees of freedom in series amino acid residues are classified.
Key wordsmolecular dynamics thermostats peptides ergodicity attractors
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