Cartesian coordinates molecular dynamics simulation

Methods and algorithms for molecular dynamics simulations of molecular fluids are described. Those techniques are emphasized that in the experience of the authors are reliable and easy to implement. This implies the use of cartesian coordinates throughout, the use of the SHAKE procedure to satisfy constraints and the incorporation of an adjustable coupling to an external bath with constant temperature and pressure. 

The remaining aspect of a trajectory simulation is choosing the initial momenta and coordinates. These initial conditions are chosen so that the results from an ensemble of trajectories may be compared with experiment and/or theory, and used to make predictions about the chemical system s molecular dynamics. In this chapter Monte Carlo methods are described for sampling the appropriate distributions for initial values of the coordinates and momenta. Trajectories may be integrated in different coordinates and conjugate momenta, such as internal [7], Jacobi [8], and Cartesian. However, the Cartesian coordinate representation is most general for systems of any size and the Monte Carlo selection of Cartesian coordinates and momenta is described here for a variety of chemical processes. Many of... 

Figure 2 Radius of convergence of different refinement methods applied to test refinements with realistic errors added to the initial model. Backbone atom r.m.s. coordinate deviations after refinement are plotted against the starting backbone atom r.m.s. coordinate deviation. The thin dashed line corresponds to refinement by conjugate gradient minimization, the thin solid line corresponds to refinement by slow-cooling simulated annealing using Cartesian molecular dynamics. The thick dot-dashed line corresponds to the average result from ten constant temperature torsion angle molecular dynamics refinements the thick solid line corresponds to the best result from each series of ten refinements...

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