A Free Energy Approach to the Torsion Dynamics of Macromolecules
Please always quote using this URN: urn:nbn:de:0297-zib-1839
- Based on the concept of free energy, we give a Hamiltonian formulation for the torsion dynamics of macromolecules. The appropriate reaction coordinates for the free energy calculations are defined in terms of soft constraints as introduced in Brooks, B.R., Zhou, J., and Reich, S., Elastic molecular dynamics with flexible constraints, in preparation and Reich, S., Smoothed Dynamics of Highly Oscillatory Hamiltonian Systems, Physica D, to appear, 1995. We consider a few simplifications that allow one to calculate the free energy analytically and to write the corresponding equations of motion as a constrained Hamiltonian system. We also discuss a possible stochastic embedding of the reduced dynamics by means of a generalized Langevin approach.
Author: | Sebastian Reich |
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Document Type: | ZIB-Report |
Date of first Publication: | 1995/06/14 |
Series (Serial Number): | ZIB-Report (SC-95-17) |
ZIB-Reportnumber: | SC-95-17 |
Published in: | Appeared under the title 'Torsion Dynamics of Molecular Systems' in: Physical Review E, vol. 53, (4), 1996, pp. 4176-4181 |