We consider the numerical treatment of Hamiltonian systems that contain a potential which grows large when the system deviates from the equilibrium value of the potential. Such systems arise, e.g., in molecular dynamics simulations and the spatial discretization of Hamiltonian partial differential equations. Since the presence of highly oscillatory terms in the solutions forces any explicit integrator to use very small step-size, the numerical integration of such systems provides a challenging task. It has been suggested before to replace the strong potential by a holonomic constraint that forces the solutions to stay at the equilibrium value of the potential. This approach has, e.g., been successfully applied to the bond stretching in molecular dynamics simulations. In other cases, such as the bond-angle bending, this methods fails due to the introduced rigidity. Here we give a careful analysis of the analytical problem by means of a smoothing operator. This will lead us to the notion...

In this paper we generalize a result by Rubin and Ungar on Hamiltonian systems containing a strong constraining potential to Langevin dynamics. Such highly oscillatory systems arise, for example, in the context of molecular dynamics. We derive constrained equations of motion for the slowly varying solution components. This includes in particular the derivation of a correcting force-term that stands for the coupling of the slow and fast degrees of motion. We will identify two limiting cases: (i) the correcting force becomes, over a finite interval of time, almost identical to the force term suggested by Rubin and Ungar (weak thermal coupling) and (ii) the correcting force can be approximated by the gradient of the Fixman potential as used in statistical mechanics (strong thermal coupling). The discussion will shed some light on the question which of the two correcting potentials is more appropriate under which circumstances for molecular dynamics. In Sec. 7, we also discuss smoothing in the context of constant temperature molecular dynamics.

Classical molecular dynamics simulation of a macromolecule requires the use of an efficient time-stepping scheme that can faithfully approximate the dynamics over many thousands of timesteps. Because these problems are highly nonlinear, accurate approximation of a particular solution trajectory on meaningful time intervals is neither obtainable nor desired, but some restrictions, such as symplecticness, can be imposed on the discretization which tend to imply good long term behavior. The presence of a variety of types and strengths of interatom potentials in standard molecular models places severe restrictions on the timestep for numerical integration used in explicit integration schemes, so much recent research has concentrated on the search for alternatives that possess (1) proper dynamical properties, and (2) a relative insensitivity to the fastest components of the dynamics. We survey several recent approaches.

Based on the concept of free energy, we derive a Hamiltonian formulation for molecular dynamics in torsion space. The appropriate reaction coordinates for the free energy calculations are defined in terms of soft constraints as introduced by B.R. Brooks, J. Zhou, and S. Reich in the context of molecular dynamics. We consider a few simplifications that allow one to calculate the free energy analytically and to write the corresponding equations of motion as a constraint Hamiltonian system that can conveniently be discretized by the well-known SHAKE algorithm. The additional computational costs, compared to using the orginal force field and constraining bond-lengths and bond-angles to their equilibrium value (hard constraints), amount, in general, to less than a complete force evaluation. We show for a single butane molecule that our Hamiltonian formulation yields the correct Boltzmann distribution in the torsion angle while the original Hamiltonian together with hard constraints on the b...

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 [3] and [14]. 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. 1

This paper makes use of statistical mechanics in order to construct

If a macromolecule is described by curvilinear coordinates or rigid constraints are imposed, the equilibrium probability density that must be sampled in Monte Carlo simulations includes the determinants of different mass-metric tensors. In this work, we explicitly write the determinant of the mass-metric tensor G and of the reduced mass-metric tensor g, for any molecule, general internal coordinates and arbitrary constraints, as a product of two functions; one depending only on the external coordinates that describe the overall translation and rotation of the system, and the other only on the internal coordinates. This work extends previous results in the literature, proving with full generality that one may integrate out the external coordinates and perform Monte Carlo simulations in the internal conformational space of macromolecules. In addition, we give a general mathematical argument showing that the factorization is a consequence of the symmetries of the metric tensors involved. Finally, the determinant of the mass-metric tensor G is computed explicitly in a set of curvilinear coordinates specially well-suited for general branched molecules. PACS: 05.20.-y, 36.10.-k, 87.14.-g, 87.15.-v, 87.15.Aa, 89.75.-k 1