A geometric approach to constrained molecular dynamics and free energy

DOI10.4310/CMS.2005.V3.N1.A1MaRDI QIDQ2567546zbMATH OpenOpenAlexFDO

Authors Carsten Hartmann, Christof Schütte

Publication date 11 October 2005

Published in Communications in Mathematical Sciences (Search for Journal in Brave)

Full work available at URL https://projecteuclid.org/euclid.cms/1111095637

zbMATH Keywords

affine connectionfree energyhybrid Monte-Carlo algorithmmetric entropymolecular dynamicsnormal connection

Mathematics Subject Classification ID

Stochastic particle methods (65C35) Holonomic systems related to the dynamics of a system of particles (70F20) Generalized coordinates; event, impulse-energy, configuration, state, or phase space for problems in mechanics (70G10) Molecular physics (81V55) Interacting particle systems in time-dependent statistical mechanics (82C22)

Review text

The authors propose a geometric approach to the determination of the mean forces along specified coordinates computed from constrained molecular dynamics. As pointed out by the authors, the result is not new, but this new approach for solving provides new interesting insight on the problem. The motion of the molecular system is driven by a Lagrangian function which is decomposed into a vertical component and a horizontal component and this decomposition is used to characterize the conditional forces from the constrained averages. The practical meaning of these force terms are exhibited in terms of coupling between the intrinsic flow and the normal vector field. This approach allows the implementation of hybrid Monte-Carlo based algorithms to compute the averaged forces.

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Cited in

(8)

• Langevin dynamics with constraints and computation of free energy differences
• Moment conditions and Bayesian non-parametrics
• Tonelli Principle: Finite Reduction and Fixed Energy Molecular Dynamics Trajectories
• Geometric and electrostatic modeling using molecular rigidity functions
• Projection of diffusions on submanifolds: Application to mean force computation
• A constrained hybrid Monte‐Carlo algorithm and the problem of calculating the free energy in several variables
• SHAKE and the exact constraint satisfaction of the dynamics of semi-rigid molecules in Cartesian coordinates, 1973--1977
• Comment on two distinct notions of free energy

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