Annealed molecular dynamics

P. Auffinger and G. Wipff, J. Comput. Chem., 11, 19 (1990). High Temperature Annealed Molecular Dynamics Simulations as a Tool for Conformational Sampling. Application to the Bicydic 222 Cryptand. 

Figure 4. Nuclear trajectories generated by the simulated annealing molecular dynamics defined by the Lagrangian in Equation(4) using masses for all parameters equal to either 0.1 or 0.01 times the proton mass. For comparison, the exact nuclear trajectory on the Born-Oppenheimer surface is shown.

Selloni et al. [48] were the first to simulate adiabatic ground state quantum dynamics of a solvated electron. The system consisted of the electron, 32 K+ ions, and 31 Cl ions, with electron-ion interactions given by a pseudopotential. These simulations were unusual in that what has become the standard simulating annealing molecular dynamics scheme, described in the previous section, was not used. Rather, the wave function of the solvated electron was propagated forward in time with the time-dependent Schrodinger equation,... 

Most of the current implementation of DFT within simulated annealing molecular dynamics calculations follows the basic outlines given in Section 1.2. Ample details particular to DFT have been given in other reviews of Car-Parrinello techniques [44-47,99]... 

Simulated annealing molecular dynamics has been used in conjunction with tight-binding Hamiltonians to model the properties of silicon [188-191], potassium [190] and carbon [190] clusters. 

Certain Schrodinger equation based methods, such as coupled cluster theory, are not based on a variational principle. They fall outside schemes that use the energy expectation value as a optimization function for simulated annealing, although these methods could be implemented within a simulated annealing molecular dynamics scheme with alternative optimization function. 

Restraints can also be incorporated into an annealed molecular dynamics protocol, performing simulations at decreasing temperatures. This approach has been used to generate protein structures consistent with NMR constraints and has recently attracted much attention for its use in solving crystal structures. In this latter application, information from the diffraction data (e.g., structure factors and phases) is incorporated as appropriate pseudo-eneigy terms in the potential energy function. 

Auffinger, P. and Wipfif, G. (1990) High temperature annealed molecular dynamics simulation as a tool for conformational sampling. J. Comput. Chem. 11 19-31. 

Niv et al. [89] have developed a method to model activated states of GPCRs using the structure-related information for fhe active state of rhodopsin and ofher GPCRs (http //physiology.med.cornell.edu/GPCRactivation/gpcrindex.html) as structural constrains for a Simulated Annealing Molecular Dynamics protocol. 

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