Polymer dynamics in torsion space
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Updated: Jun 17, 2026

Synthesis of Cyclic Polymers and Characterization of Their Diffusive Motion in the Melt State at the Single Molecule Level
Published on: September 26, 2016
Krister O E Henriksson1, Janne Pesonen
1Department of Chemistry, P. O. Box 55, F1-00074 University of Helsinki, Finland. krister.henriksson@helsinki.fi
Abstract:
The large scale motion of proteins, or covalently bonded polymers in general, is governed by the dynamics of the torsion angles, with bond lengths and bond angles kept approximately constant. In the present work, the Lagrangian equations of torsion motion are derived for a general macromolecule. The dynamics is implemented numerically for a test protein, using the velocity Verlet method as the integrator. The results indicate time steps of up to about 30 fs can be used for short time (up to at least 20 ps) simulations, before the dynamics and energy start to differ significantly from results obtained with smaller time steps. For longer time simulations, up to 1000 ps, a time step of 10 fs is relatively safe.
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