Molecular dynamics applications

Goodfellow J M 1990 Molecular Dynamics—Applications in Molecular Biology (Boca Raton, FL Chemioal Rubber Company)... 

R. D. Skeel, G. H. Zhang, and T. Schlick. A family of symplectic integrators Stability, accuracy, and molecular dynamics applications. SIAM J. Scient. COMP., 18 203-222, 1997. 

In molecular dynamics applications there is a growing interest in mixed quantum-classical models various kinds of which have been proposed in the current literature. We will concentrate on two of these models the adiabatic or time-dependent Born-Oppenheimer (BO) model, [8, 13], and the so-called QCMD model. Both models describe most atoms of the molecular system by the means of classical mechanics but an important, small portion of the system by the means of a wavefunction. In the BO model this wavefunction is adiabatically coupled to the classical motion while the QCMD model consists of a singularly perturbed Schrddinger equation nonlinearly coupled to classical Newtonian equations, 2.2. 

Garcia-Vela, A., Gerber, R. B. Hybrid quantum-semiclassical wave packet method for molecular dynamics Application to photolysis of Ar...HCl. J. Chem. Phys. 98 (1993) 427-43... 

J. A. Board, Jr. et al.. Scalable variants of Multipole-Accelerated Algorithms for Molecular Dynamics Applications, Proceedings, Seventh SIAM Conference on Parallel Processing for Scientific Computing, SIAM, Philadelphia (1995), pp. 295-300. 

Molecular Workbench (MW) is a two-dimensional molecular dynamics application written in Java and created by Concord Consortium (http //workbench.concord.org/). It provides multiple representations and molecular dynamic simulations that allow... 

Molecular Dynamics Applications in Molecular Biology, J. M. Goodfellow, ed., CRC Press, Boca Raton, FL, 1990. 

Singh, U. C., Brown, F. K., Bash, P. A., and Kollman, P. A. An approach to the application of free energy perturbation methods using molecular dynamics applications to the transformations of CH3OH —> CH3CH3, H3O+ —> NH4, glycine... 

V. Dubois, P. Umari, and A. Pasquarello (2004) Dielectric susceptibility of dipolar molecular liquids by ab initio molecular dynamics application to liquid HCl. Chem. Phys. Lett. 390, p. 193... 

Khelashvili, G., Pandit, S.A., Scott, H.L. Self-consistent mean-field model based on molecular dynamics Application to lipid-cholesterol bilayers. J. Chem. Phys. 2005,123, 034910. 

M. Billeter, A, E. Howard, 1. D. Kuntz, and P. A. Kollman,/. Am. Chem. Soc., 110, 8383 (1988), A New Technique to Calculate Low-Energy Conformations of Cyclic Molecules Utilizing the Ellipsoid Algorithm and Molecular Dynamics Application to 18-Crown-6. 

D. Brown and J. H. R. Clarke, /. Chem. Phys., 92, 3062 (1990). A Direct Method of Studying Reaction Rates by Equilibrium Molecular Dynamics Application to the Kinetics of Isomerization in Liquid -Butane. 

An Approach to the Application of Free Energy Perturbation Methods Using Molecular Dynamics Applications to the Transformations of CH3OH—CH3CH3, H3O+— NH4, Glycine-Alanine, and Alanine-Phenylalanine in Aqueous Solution and to H30 + (H20)3—NH4+(H20)3 in the Gas Phase. 

In many molecular dynamics applications, the system may be decomposed as H q.p) = p M p/2 + Usiq) + where Us, is a soft potential, in which the natural motion would be relatively slow, whereas f/p is a much stronger term which would give rise to relatively rapid motion. We further suppose Us (with its gradient) is expensive to compute, perhaps because it involves many terms, whereas 17f is relatively simple. Because U requires small timesteps, we think of separating the calculation of a timestep, typically in a symmetric form. Let denote the map associated to the Verlet method for the system witliout Us, using a stepsize fr. 

In typical molecular dynamics applications with multiple bodies and complicated force laws, the motion is assumed to be chaotic. Ergodic coverage of would then have to arise from the global properties of a chaotic system (sensitivity to initial conditions and transitivity). Liouville s equation,... 

As the focus of this chapter is on the computation of averages, the concept of weak order is more appropriate in evaluating methods. Yet, even the weak order of convergence may not be suitable in molecular dynamics applications, or rather, we are interested in the very long term behavior of the weak error which is governed by the coefficient T)(t) as r oo [270,356]. 

As such, we return now to the harmonic oscillator, which as well as being the simplest molecular model is also one of the most relevant for molecular dynamics applications, as many issues of stability and timestep in molecular dynamics simulations arise due to harmonic potentials used to model covalent bonds (such as in crystalline solids and biomolecules). The canonical distributions of position and momentum are also of a simple form (Gaussians), making such oscillators particularly amenable to analysis. 

Continual advances in computer technology and the development of new algorithms have greatly broadened the range, in size and complexity, of systems that can be simulated by molecular dynamics. Applications of the techniques discussed in this chapter have already yielded many important results, and we expect molecular dynamics to remain a valuable tool in the furthering of our understanding of fundamental dynamical processes. 

Inclusion of Reaction Fields in Molecular Dynamics Application to Liquid Water. 

M. Karplus, Molecular Dynamics Applications to Proteins , ed. J. L. Rivail, Modelling of Molecular Structures and Properties , Elsevier Science Publishers, Amsterdam, 1990, pp. 427-461. 

Thus, in general, most properties calculated by molecular mechanics and molecular dynamics applications ultimately require the use of the force field s energy expression. 

A. Bhatele, L. V. Kale, and S. Kumar. Dynamic Topology Aware Load Balancing Algorithms for Molecular Dynamics Applications, Proceedings of the 23rd International Conference on Supercomputing (ICS 09), 110 (2009). 

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