Molecular dynamics time step size

The SDEL algorithm allows the computation of atomically detailed trajectories connecting two known conformations of the molecule over long time scales. In contrast to normal and MTS molecular dynamics algorithms, step sizes can be increased easily by two or three orders of magnitude without... 

An interesting approach has recently been chosen in the MBO(N)D program ([Moldyn 1997]). Structural elements of different size varying from individual peptide planes up to protein domains can be defined to be rigid. During an atomistic molecular dynamics simulation, all fast motion orthogonal to the lowest normal modes is removed. This allows use of ca. 20 times longer time steps than in standard simulations. 

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]. 

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 ... 

In many molecular dynamics simulations, equilibration is a separate step that precedes data collection. Equilibration is generally necessary to avoid introducing artifacts during the heating step and to ensure that the trajectory is actually simulating equilibrium properties. The period required for equilibration depends on the property of interest and the molecular system. It may take about 100 ps for the system to approach equilibrium, but some properties are fairly stable after 10-20 ps. Suggested times range from 5 ps to nearly 100 ps for medium-sized proteins. 

Fig. 6.10. Comparison of overlap sampling and FEP calculation results for the free energy change along the mutation of an adenosine in aqueous solution (between A = 0.05 and 0.45) in a molecular dynamics simulation. The results represent the average behavior of 14 independent runs. (MD time step.) The sampling interval is 0.75 ps. The upper half of the plot presents the standard deviation of the mean (with gives statistical error) for AA as a function of sample size N the lower half of the plot gives the estimate of A A - for comparison of the accuracy, the correct value of AA is indicated by the bold horizontal line...

The need for computer simulations introduces some constraints in the description of solvent-solvent interactions. A simulation performed with due care requires millions of moves in the Monte Carlo method or an equivalent number of time steps of elementary trajectories in Molecular Dynamics, and each move or step requires a new calculation of the solvent-solvent interactions. Considerations of computer time are necessary, because methodological efforts on the calculation of solvation energies are motivated by the need to have reliable information on this property for a very large number of molecules of different sizes, and the application of methods cannot be limited to a few benchmark examples. There are essentially two different strategies. 

Select the Molecular dynamics menu to open the dialog box. Specify Time, Temperature, and Step size for Heating cycle, Equilibrium period, and Cooling cycle. 

The same applies, in different form though, to a molecular dynamics procedure. The random elements here are the starting point and the initial velocities of the atoms. More or less arbitrarily chosen is the size of the time steps At. 

The earliest molecular dynamics (MD) simulations on polyatomic molecular systems date back less than three decades. Since then, MD simulations have been applied to increasingly more complex molecules, such as n-alkanes" " and proteins. " In contrast to the earlier simulations of atomic systems, the simulation of polyatomic molecules is complicated by the existence of both intramolecular and intermolecular degrees of freedom. The presence of this variety of degrees of freedom leads to a wide range of time scales of molecular motions. Because the size of the time step used in MD simulations is limited by the shortest period of motion present, simulations of long time scale... 

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