Multiple time-step

A straightforward derivation (not reproduced here) shows that the effect of the diree successive steps embodied in equation (b3.3.7), with the above choice of operators, is precisely the velocity Verlet algorithm. This approach is particularly usefiil for generating multiple time-step methods. 

Some people prefer to use the multiple time step approach to handle fast degrees of freedom, while others prefer to use constraints, and there are situations in which both techniques are applicable. Constraints also find an application in the study of rare events, where a system may be studied at the top of a free energy barrier (see later), or for convenience when it is desired to fix a thennodynamic order parameter or ordering direction... 

MD, one needs to use multiple time step methods to ensure proper handling of the sprmg vibrations, and there is a possible physical bottleneck in the transfer of energy between the spring system and the other degrees of freedom which must be handled properly [199]. In MC, one needs to use special methods to sample configuration space efficiently [200, 201]. 

Abstract. Molecular dynamics (MD) simulations of proteins provide descriptions of atomic motions, which allow to relate observable properties of proteins to microscopic processes. Unfortunately, such MD simulations require an enormous amount of computer time and, therefore, are limited to time scales of nanoseconds. We describe first a fast multiple time step structure adapted multipole method (FA-MUSAMM) to speed up the evaluation of the computationally most demanding Coulomb interactions in solvated protein models, secondly an application of this method aiming at a microscopic understanding of single molecule atomic force microscopy experiments, and, thirdly, a new method to predict slow conformational motions at microsecond time scales. 

As an example for an efficient yet quite accurate approximation, in the first part of our contribution we describe a combination of a structure adapted multipole method with a multiple time step scheme (FAMUSAMM — fast multistep structure adapted multipole method) and evaluate its performance. In the second part we present, as a recent application of this method, an MD study of a ligand-receptor unbinding process enforced by single molecule atomic force microscopy. Through comparison of computed unbinding forces with experimental data we evaluate the quality of the simulations. The third part sketches, as a perspective, one way to drastically extend accessible time scales if one restricts oneself to the study of conformational transitions, which arc ubiquitous in proteins and are the elementary steps of many functional conformational motions. 

In general, multiple-time-step methods increase computational efficiency in a way complementary to multipole methods The latter make use of regularities in space, whereas multiple-time-stepping exploits regularities in time. Figure 2 illustrates the general idea ... 

Fig. 2. Distance classes j = 0,1, 2,... (left) are defined for an atom (central dot) by a set of radii Rj+i the right cnrves sketch the temporal evolntion of the tot il force acting on the selected atom originating from cill atoms in distance class j shown are the exact forces (solid line), their exact valnes to be computed within the multiple time step scheme (filled squares), linear force extrapolations (dotted lines), and resulting force estimates (open sqnares).

Additionally, to optimize task 4, we applied a conventional, atom pair interaction based multiple-time-step scheme to the force computation within Ihe innermost distance class. Here, for atom pairs closer than 5 A, the Coulomb sum is calculated every step, and for all other atom pairs the Coulomb sum is extrapolated every second step from previously explicitly calculated forces. 

For large systems comprising 36,000 atoms FAMUSAMM performs four times faster than SAMM and as fast as a cut-off scheme with a 10 A cut-off distance while completely avoiding truncation artifacts. Here, the speed-up with respect to SAMM is essentially achieved by the multiple-time-step extrapolation of local Taylor expansions in the outer distance classes. For this system FAMUSAMM executes by a factor of 60 faster than explicit evaluation of the Coulomb sum. The subsequent Section describes, as a sample application of FAMUSAMM, the study of a ligand-receptor unbinding process. 

W. B. Streett, D. J. Tildesley, and G. Saville. Multiple time step methods in molecular dynamics. Mol. Phys., 35 639-648, 1978. 

D. D. Humphreys, R. A. Friesner, and B. J. Berne. Simulated annealing of a protein in a continuum solvent by multiple-time-step molecular dynamics. J. Phys. Chem., 99 10674-10685, 1995. 

M. Watanabe and M. Karplus. Dynamics of molecules with internal degrees of freedom by multiple time-step methods. J. Chem. Phys., 99 8063-8074, 1993. 

J. J. Biesiadecki and R. D. Skeel. Dangers of multiple-time-step methods. J. Comp. Phys., 109 318-328, 1993. 

Another way to overcome the step-size restriction fc < is to use multiple-time-stepping methods [4] or implicit methods [17, 18, 12, 3). In this paper, we examine the latter possibility. But for large molecular systems, fully implieit methods are very expensive. For that reason, we foeus on the general class of scmi-implicit methods depicted in Fig. 1 [12]. In this scheme. Step 3 of the nth time step ean be combined with Step 1 of the (n - - l)st time step. This then is a staggered two-step splitting method. We refer to [12] for further justification. 

Since many systems of interest in chemistry have intrinsic multiple time scales it is important to use integrators that deal efficiently with the multiple time scale problem. Since our multiple time step algorithm, the so-called reversible Reference System Propagator Algorithm (r-RESPA) [17, 24, 18, 26] is time reversible and symplectic, they are very useful in combination with HMC for constant temperature simulations of large protein systems. 

Fig. 1. Schematic for the impulse multiple time stepping method.

T. R. Littell, R. D. Skeel, and M. Zhang. Error analysis of symplectic multiple time stepping. SIAM J. Numer. Anal., 34 1792-1807, 1997. 

Wisdom, J. The Origin of the Kirkwood Gaps A Mapping for Asteroidal Motion Near the 3/1 Commensurability. Astron. J. 87 (1982) 577-593 Tuckerman, M., Martyna, G. J., Berne, J. Reversible Multiple Time Scale Molecular Dynamics. J. Chem. Phys. 97 (1992) 1990-2001 Tuckerman, M., Berne, J. Vibrational Relaxation in Simple Fluids Comparison of Theory and Simulation. J. Chem. Phys. 98 (1993) 7301-7318 Humphreys, D. D., Friesner, R. A., Berne, B. J. A Multiple-Time Step Molecular Dynamics Algorithm for Macromolecules. J. Chem. Phys. 98 (1994) 6885-6892... 

Watanabe, M., Karplus, M. Dynamics of Molecules with Internal Degrees of Freedom by Multiple Time-Step Methods. J. Chem. Phys. 99 (1995) 8063-8074 Figueirido, F., Levy, R. M., Zhou, R., Berne, B. J. Large Scale Simulation of Macromolecules in Solution Combining the Periodic Fast Multiple Method with Multiple Time Step Integrators. J. Chem. Phys. 106 (1997) 9835-9849 Derreumaux, P., Zhang, G., Schlick, T, Brooks, B.R. A Truncated Newton Minimizer Adapted for CHARMM and Biomolecular Applications. J. Comp. Chem. 15 (1994) 532-555... 

Long term simulations require structurally stable integrators. Symplec-tic and symmetric methods nearly perfectly reproduce structural properties of the QCMD equations, as, for example, the conservation of the total energy. We introduced an explicit symplectic method for the QCMD model — the Pickaback scheme— and a symmetric method based on multiple time stepping. 

Symplectic Multiple-Time-Stepping Integrators for Quantum-Classical Molecular Dynamics... 

Abstract. The overall Hamiltonian structure of the Quantum-Classical Molecular Dynamics model makes - analogously to classical molecular dynamics - symplectic integration schemes the methods of choice for long-term simulations. This has already been demonstrated by the symplectic PICKABACK method [19]. However, this method requires a relatively small step-size due to the high-frequency quantum modes. Therefore, following related ideas from classical molecular dynamics, we investigate symplectic multiple-time-stepping methods and indicate various possibilities to overcome the step-size limitation of PICKABACK. 

Here we suggest a different approach that propagates the system using multiple step-sizes, i.e., few steps with step-size At are taken in the slow classical part whereas many smaller steps with step-size 5t are taken in the highly oscillatory quantum subsystem (see, for example, [19, 4] for symplectic multiple-time-stepping methods in the context of classical molecular dynamics). Therefore, we consider a splitting of the Hamiltonian H = Hi +H2 in the following way ... 

Upon computing the eigenvalues of the operator H(q), the equations (3)-(5) can be solved exactly. However, this is, in general, an expensive undertaken. Therefore we proceed with the following multiple-time-stepping approach The first step is to consider the identity... 

We have derived time-reversible, symplectic, and second-order multiple-time-stepping methods for the finite-dimensional QCMD model. Theoretical results for general symplectic methods imply that the methods conserve energy over exponentially long periods of time up to small fluctuations. Furthermore, in the limit m —> 0, the adiabatic invariants corresponding to the underlying Born-Oppenheimer approximation will be preserved as well. Finally, the phase shift observed for symmetric methods with a single update of the classical momenta p per macro-time-step At should be avoided by... 

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