Molecular modeling energy minimization, dynamics simulation

Model optimization is a further refinement of the secondary and tertiary structure. At a minimum, a molecular mechanics energy minimization is done. Often, molecular dynamics or simulated annealing are used. These are frequently chosen to search the region of conformational space relatively close to the starting structure. For marginal cases, this step is very important and larger simulations should be run. 

Molecular modeling using either Monte-Carlo simulations or molecular dynamics is used to apply molecular mechanics energy minimizations to very complex systems [348]. In complex flexible molecules such as proteins or nucleic adds, the number of variable parameters, i.e., bond torsion angles, is such that the global search for energy minima becomes impossible The same problem occurs with theoretical calculations of water structure in aqueous solutions or in heavily hydrated crystals. 

The size, location, and structure of platinum clusters in H-mordenite were modeled by molecular mechanics energy minimization and molecular dynamics simulation techniques [96G1]. It was suggested that the relative stability of monoatomic platinum sites in aluminosilicate mordenites is related to the specific aluminum insertion in T sites of the framework structure. The structural features of the platinum cluster confined to the 12-ring main channel are almost independent of the total Pt content and strongly dependent upon the surrounding zeolite structural field. 

Molecular simulations, including energy minimizations, dynamics, and firee energy perturbation calculations on macromolecules. Quest for ab initio molecular orbital calculations. Ultimol for molecular visualizations. Galaxy for Hansch-type and 3D QSAR and molecular modeling. 

Tel. 415-476-4637, fax 415-476-0688, e-mail pak cgl.ucsf.edu Assisted Model Building using Energy Refinement. Energy minimization, molecular dynamics, and free energy perturbation (FEP) calculations. SPASMS (San Francisco Package of Applications for the Simulation of Molecular Systems). VAX, Cray versions. 

In this chapter, we present new results based on semi-empirical quantum calculations (PM3) that include solvation and charging effects simultaneously on the same model SFA.71 These calculations were carried out in HyperChem 5.0 (Hypercube, Inc.). Solvation was carried out with two approaches. In the first approach, the neutral, gas-phase SFA model was simulated, then this molecule was deprotonated at each of four carboxylic acid sites. Finally, a solvation sphere of H20 molecules was used to surround the anionic SFA and the structure obtained via molecular dynamics simulations and energy minimizations as an isolated nanodroplet. This approach has the advantage of allowing maximum flexibility of the model SFA. Larger model systems may require long simulation runs to sample all available conformations, but isolation of the SFA and water allows each component to move more freely. 

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