Multiple molecular dynamics method

Rc This deviation has been observed by multiple researchers, using off-lattice molecular dynamics methods and the S-BFM. In the case of S-BFM, the deviation is independent of equilibration method. Suzuki et al. (2009) presented an alternate expression for the free energy due to the catenation constraint as... 

Woo TK, Margl P, Blochl PE, Ziegler T (2002) Sampling phase space by a combined QM/MM ab initio Car-Parrinello molecular dynamics method with different (multiple) time steps in the quantum mechanical (QM) and molecular mechanical (MM) domains. J Phys Chem A 106 1173-1182... 

Figure 3 Time dependent root mean square (rms) deviation. from the starting crystal structure for the three different sets of multiple molecular dynamics (MMD) trajectories of the tRNA " anticodon hairpin, each using a different method for the evaluation of the electrostatic long-range interactions. The model increases in accuracy from the top graph to the bottom one...

The abbreviation for reference system propagator. An approach to solve for the positions and velocities of a complex system using multiple time steps to improve the efficiency of molecular dynamics methods for very large systems. 

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. 

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

Methods for Dealing with the Intrinsic Multiple Time Scale Problem in 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 ... 

Other methods which are applied to conformational analysis and to generating multiple conformations and which can be regarded as random or stochastic techniques, since they explore the conformational space in a non-deterministic fashion, arc genetic algorithms (GA) [137, 1381 simulation methods, such as molecular dynamics (MD) and Monte Carlo (MC) simulations 1139], as well as simulated annealing [140], All of those approaches and their application to generate ensembles of conformations arc discussed in Chapter II, Section 7.2 in the Handbook. 

To overcome the limitations of the database search methods, conformational search methods were developed [95,96,109]. There are many such methods, exploiting different protein representations, objective function tenns, and optimization or enumeration algorithms. The search algorithms include the minimum perturbation method [97], molecular dynamics simulations [92,110,111], genetic algorithms [112], Monte Carlo and simulated annealing [113,114], multiple copy simultaneous search [115-117], self-consistent field optimization [118], and an enumeration based on the graph theory [119]. 

Hudock et al. [126] used the ab initio molecular dynamics multiple spawning method to go beyond the static picture based on PES and include the time dependent dynamical behavior and predict time-resolved photoelectron spectroscopy results. According to these results the first ultrafast component of the photoelectron spectra of uracil corresponds to relaxation on the S2 minimum rather than nonadiabatic transitions to the Si state. The authors suggest that the radiationless relaxation from... 

In such cases, the MEHMC method could be employed in combination with an enhanced sampling method that deforms the effective energy surface (but preserves the location of the potential minima), such as that in [29, 97]. Likewise, it may be worthwhile to explore the use of a reversible multiple-time-scale molecular dynamics propagator [103] with MEHMC to accelerate the dynamical propagation. 

There is a need for large-scale differential-algebraic methods for simulating systems at multiple scales (e.g., fluid mechanics and molecular dynamics), a capability that is still at a very early stage. 

Localized molecular orbital/generalized valence bond (LMO/GVB) method, direct molecular dynamics, ab initio multiple spawning (AIMS), 413-414 Longuet-Higgins phase-change rule conical intersections ... 

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