Verlet integrator

Verlet, L. Computer experiments on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules. Phys. Rev. 165 (1967) 98-103. Ryckaert, J.-P., Ciccotti,G., Berendsen, H.J.C. Numerical integration of the cartesian equations of motion of a system with constraints Molecular dynamics of n-alkanes. Comput. Phys. 23 (1977) 327-341. 

Accuracy, however, in biomolecular trajectories, must be defined somewhat subjectively. In the absence of exact reference data (from experiment or from an analytical solution), the convention has been to measure accuracy with respect to reference trajectories by a Verlet-like integrator [18, 19] at a timestep of 1 or 0.5 fs (about one tenth or one twentieth the period, respectively, of the fastest period an 0-H or N-H stretch). As pointed out by Deufihard et al. [20], these values are still larger than those needed to... 

This discussion suggests that even the reference trajectories used by symplectic integrators such as Verlet may not be sufficiently accurate in this more rigorous sense. They are quite reasonable, however, if one requires, for example, that trajectories capture the spectral densities associated with the fastest motions in accord to the governing model [13, 15]. Furthermore, other approaches, including nonsymplectic integrators and trajectories based on stochastic differential equations, can also be suitable in this case when carefully formulated. 

Another view of this theme was our analysis of spectral densities. A comparison of LN spectral densities, as computed for BPTI and lysozyme from cosine Fourier transforms of the velocity autocorrelation functions, revealed excellent agreement between LN and the explicit Langevin trajectories (see Fig, 5 in [88]). Here we only compare the spectral densities for different 7 Fig. 8 shows that the Langevin patterns become closer to the Verlet densities (7 = 0) as 7 in the Langevin integrator (be it BBK or LN) is decreased. 

In this paper, we discuss semi-implicit/implicit integration methods for highly oscillatory Hamiltonian systems. Such systems arise, for example, in molecular dynamics [1] and in the finite dimensional truncation of Hamiltonian partial differential equations. Classical discretization methods, such as the Verlet method [19], require step-sizes k smaller than the period e of the fast oscillations. Then these methods find pointwise accurate approximate solutions. But the time-step restriction implies an enormous computational burden. Furthermore, in many cases the high-frequency responses are of little or no interest. Consequently, various researchers have considered the use of scini-implicit/implicit methods, e.g. [6, 11, 9, 16, 18, 12, 13, 8, 17, 3]. 

The constrained equations of motion in cartesian eoordinates can be solved by the SHAKE or (the essentially equivalent) RATTLE method (see [8]) which requires the solution of a non-linear system of equations in the Lagrange multiplier funetion A. The equivalent formulation in local coordinates ean still be integrated by using the explicit Verlet method. 

One of the advantages of the Verlet integrator is that it is time reversible and symplectic[30, 31, 32]. Reversibility means that in the absence of numerical round off error, if the trajectory is run for many time steps, say nAt, and the velocities are then reversed, the trajectory will retrace its path and after nAt more time steps it will land back where it started. An integrator can be viewed as a mapping from one point in phase apace to another. If this mapping is applied to a measurable point set of states at on(> time, it will... 

This procedure is then repeated after each time step. Comparison with Eq. (2) shows that the result is the velocity Verlet integrator and we have thus derived it from a split-operator technique which is not the way that it was originally derived. A simple interchange of the Ly and L2 operators yields an entirely equivalent integrator. 

This article is organized as follows Sect. 2 explains why it seems important to use symplectic integrators. Sect. 3 describes the Verlet-I/r-RESPA impulse MTS method, Sect. 4 presents the 5 femtosecond time step barrier. Sect. 5 introduce a possible solution termed the mollified impulse method (MOLLY), and Sect. 6 gives the results of preliminary numerical tests with MOLLY. 

The application in [24] is to celestial mechanics, in which the reduced problem for consists of the Keplerian motion of planets around the sun and in which the impulses account for interplanetary interactions. Application to MD is explored in [14]. It is not easy to find a reduced problem that can be integrated analytically however. The choice /f = 0 is always possible and this yields the simple but effective leapfrog/Stormer/Verlet method, whose use according to [22] dates back to at least 1793 [5]. This connection should allay fears concerning the quality of an approximation using Dirac delta functions. 

The simplest of the numerical techniques for the integration of equations of motion is leapfrog-Verlet algorithm (LFV), which is known to be symplectic and of second order. The name leapfrog steams from the fact that coordinates and velocities are calculated at different times. 

Janezic, D. Trobec, R. Parallelization of an Implicit Runge-Kutta Method for Molecular Dynamics Integration. J. Chem. Inf. Comput. Sci. 34 (1994) 641-646 R. Trobec and D. Janezic Comparison of Parallel Verlet and Implicit Runge-Kutta Method for Molecular Dynamics Integration. J. Chem. Inf. Comp. Sci., 35 (1995) 100-105... 

Hence, as the second class of techniques, we discuss adaptive methods for accurate short-term integration (Sec. 4). For this class, it is the major requirement that the discretization allows for the stepsize to adapt to the classical motion and the coupling between the classical and the quantum mechanical subsystem. This means, that we are interested in discretization schemes which avoid stepsize restrictions due to the fast oscillations in the quantum part. We can meet this requirement by applying techniques recently developed for evaluating matrix exponentials iteratively [12]. This approach yields an adaptive Verlet-based exponential integrator for QCMD. 

Using the symmetric Verlet algorithm for integrating exp(rL ) yields ... 

Fig. 3. Stepsize r used in the simulation of the collinear photo dissociation of ArHCl the adaptive Verlet-baaed exponential integrator using the Lanczos iteration (dash-dotted line) for the quantum propagation, and a stepsize controlling scheme based on PICKABACK (solid line). For a better understanding we have added horizontal lines marking the collisions (same tolerance TOL). We observe that the quantal H-Cl collision does not lead to any significant stepsize restrictions.

The standard numerical integrators for the constrained system (12) are the SHAKE scheme [23], which extends the Verlet method (2),... 

The Beeman integration scheme uses a more accurate expression for the velocity. As a consequence it often gives better energy conservation, because the kinetic energy is calculated directly from the velocities. However, the expressions used are more complex than those of the Verlet algorithm and so it is computationally more expensive. 

The underlying theory of r-RESPA is somewhat involved, but the final result and const quent implementation is actually rather straightforward, being very closely related to th velocity Verlet integration scheme. For our four-way decomposition the algorithm woul... 

Our discussion so far has considered the use of SHAKE with the Verlet algorithm Versions have also been derived for other integration schemes, such as the leap-froj algorithm, the predictor-corrector methods and the velocity Verlet algorithm. In the cast of the velocity Verlet algorithm, the method has been named RATTLE [Anderson 1983]... 

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