Dynamics Systems, Molecular

The first chapter, on Conformational Dynamics, includes discussion of several rather recent computational approaches to treat the dominant slow modes of molecular dynamical systems. In the first paper, SCHULTEN and his group review the new field of steered molecular dynamics (SMD), in which large external forces are applied in order to be able to study unbinding of ligands and conformation changes on time scales accessible to MD... 

Since A, B, and C are regions in the phase space of single closed system, the transitions between A and represent a unimolecular reaction or isomerization, rather than a general reaction in the sense of chemical kinetics. Unlike some unimolecular reactions, (e.g the decomposition of diatomic molecules) the molecular dynamics system of eq. 1 will be assumed to have sufficiently many well-coupled degrees of freedom that transitions between reactant and product regions occur spontaneously, without outside interference. 

There are a wide variety of techniques that can be utilized to bias the volume equation of motion to yield only compressive shock solutions. Here we present two techniques that we have implemented for various molecular dynamics systems. One of these techniques involves modifying the Hamiltonian to apply a constant external pressure at when v > Vg. In this case, the volume equation of motion (Eq. (16)) becomes,... 

In addition to periodic image interaction effects, there is an additional factor in choosing the computational cell size that must be considered when using this shock molecular dynamics technique. The connection to continuum theory is based on the assumption that the simulated material element (molecular dynamics system) is sufficiently small that stress. 

The sections above describe the simulation of a single stable shock wave. However, it is not always possible for a single shock to take the molecular dynamics system to some pressures or particle velocities. For example. Figure 2 shows how it may not be possible to connect a straight Rayleigh line to all final pressures when there is a region of negative... 

Figure 8 shows the volume as a function of time for four overdriven single shock wave simulations in the [110] direction of a 25688 atom perfect Lennard-Jones face centered cubic crystal. Elastic compression is characterized by VjV 0.9 and plastic compression occurs for smaller volumes. As the shock speed decreases, the amount of time the molecular dynamics system spends in the elastically compressed state increases. This plot illustrates how the final thermodynamic state in the shock is a function of the simulation duration when slow chemical reactions or phase transitions occur. For example, on the 10-20 ps timescale, the 2.8 km/sec shock has an elastically compressed final state on the 100 ps timescale, this simulation has a plastically compressed final state. 

In this chapter we have presented a multi-scale method for molecular dynamics simulations of shock compression and characterized its behaviour. This method attempts to constrain the molecular dynamics system to the sequence of thermodynamic states that occur in a shock wave. While we have presented one particular approach, it is certainly not unique and there are likely a variety of related approaches to multi-scale simulations that have a variety of differing practical properties. These methods open the door to simulations of shock propagation on the longest timescales accessible by molecular d5nnamics and the use of accurate but computationally costly material descriptions like density fimctional theory. It is our belief that this method promises to be a valuable tool for elucidation of new science in shocked condensed matter. 

As shown in Figure 26.3, both lattice Boltzmann gas (LBG) [37,38], direct simulation Monte-Carlo (DSM-C) [41], and off-grid particle methods such as DPD [42], and fluid particle method (FPM) [43] can be treated within a common methodological framework. This framework in the mesoscale consists the successive coarse-graining of the underlying molecular dynamics system. We can list its components as ... 

In some molecular dynamics work, the process of equilibration has accounted for a substantial fraction of the total computer time devoted to the calculation. If the intermolecular potential has a sufficiently short range, however, it is possible to use only a fraction of the molecular dynamics system for equilibration. One can set aside a subsystem containing, say, an eighth of the total number of molecules, select initial conditions, and allow the... 

If C t) is a time correlation function of a single-particle property, then in addition to time averaging, C t) may be averaged over the N particle labels in the molecular dynamics system. This additional averaging decreases the error by the factor (1/N). Even if C(t) is the time correlation function of a... 

Fijany A et al (1998) Novel algorithms for massively parallel, long-term, simulation of molecular dynamics systems. Adv Eng Softw 29(3-6) 441-450... 

Lipid Properties and the Orientation of Aromatic Residues in OmpF, Influenza M2, and Alamethicin Systems Molecular Dynamics Systems. 

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