Molecular dynamics trajectory model

In molecular mechanics and molecular dynamics studies of proteins, assig-ment of standard, non-dynamical ionization states of protein titratable groups is a common practice. This assumption seems to be well justified because proton exchange times between protein and solution usually far exceed the time range of the MD simulations. We investigated to what extent the assumed protonation state of a protein influences its molecular dynamics trajectory, and how often our titration algorithm predicted ionization states identical to those imposed on the groups, when applied to a set of structures derived from a molecular dynamics trajectory [34]. As a model we took the bovine... 

Finite difference techniques are used to generate molecular dynamics trajectories with continuous potential models, which we will assume to be pairwise additive. The essential idea is that the integration is broken down into many small stages, each separated in time by a fixed time 6t. The total force on each particle in the configuration at a time t is calculated as the vector sum of its interactions with other particles. From the force we can determine the accelerations of the particles, which are then combined with the positions and velocities at a time t to calculate the positions and velocities at a time t + 6t. The force is assumed to be constant during the time step. The forces on the particles in their new positions are then determined, leading to new positions and velocities at time t - - 2St, and so on. 

There are therefore four adjustable parameters per atom in the refinement (xy, yy, Zj, By). In the computer experiments we have carried out to test the assumptions of the nucleic acid refinement model we have generated sets of observed structure factors F (Q), from the Z-DNA molecular dynamics trajectories. The thermal averaging implicit in Equation III.3 is accomplished by averaging the atomic structure factors obtained from coordinate sets sampled along the molecular dynamics trajectories at each temperature ... 

A theoretical analysis of the possible conformations of polylp-phenylene terephthalate) (PPTA) and polylp-phenylene isophthalate) (PPIA) is performed on the basis of molecular mechanics and molecular dynamics trajectories. The dependence of the persistence length on the fluctuations of the torsional angle around the ester bond is discussed for PPTA in the frame of the RIS model. Realistic parameters like bond length and bond angles are provided by computer simulations using MD. 

Recently, Garth Jones (UNSW) and his co-workers have described a semi-classical molecular dynamics (MD) model, which incorporates the trajectory surface hopping (TSH) method, that shows promise in investigating a number of important problems concerning the effects of molecular vibrations on the dynamics of ET reactions, including formally symmetry-forbidden ones. Essentially,... 

Tel. 312-327-9390, e-mail tj bert.eecs.uic.edu General purpose graphics and animation toolkit for molecular models, such as stick figures, ball-and-stick, CPK, dot surfaces, wire-mesh surfaces, and fully shaded polygon surfaces. Animation of molecular dynamics trajectories. Silicon Graphics. 

Molecular model-building (conformational search) methods fall into two general classes systematic and random. - Systematic methods search all possible combinations of torsional angles, whereas random methods usually involve a Monte Carlo (with Metropolis sampling ) or molecular dynamics trajectory. Both approaches attempt to search large areas of conformational space and eventually converge on the desired conformation or structure. Dis-... 

Finite difference techniques are used to generate molecular dynamics trajectories with continuous potential models, which we will assume to be pairwise additive. The essential idea is that the integration is broken down into many small stages, each separated in time by a fixed time fit. The total force on each particle in the configuration at a time t is... 

A model of immiscible Lennard-Jones atomic solvents has been used to study the adsorption of a diatomic solute [71]. Subsequently, studies of solute transfer have been performed for atoms interacting through Lennard-Jones potentials [69] and an ion crossing an interface between a polar and a nonpolar liquid [72]. In both cases the potential of mean force experienced by the solute was computed the results of the simulation were compared with the result from the transition state theory (TST) in the first case, and with the result from a diffusion equation in the second case. The latter comparison has led to the conclusion that the rate calculated from the molecular dynamics trajectories agreed with the rate calculated using the diffusion equation, provided the mean-force potential and the diffusion coefficient were obtained from the microscopic model. 

The first computations of ionization constants of residues in proteins for structures derived from molecular dynamics trajectories were described by Wendoloski and Matthew for tuna cytochrome c. In that study, conformers were generated using molecular dynamics simulations with a range of solvents, simulating macroscopic dielectric formalisms, and one solvent model that explicitly included solvent water molecules. The authors calculated individual pR values, overall titration curves, and electrostatic potential surfaces for average structures and structures along each simulation trajectory. However, the computational scheme for predicting electrostatic interactions in proteins used by Wendoloski and Matthew was not based on a FDPB model but on the modified Tanford-Kirkwood approach, which is not discussed in this chapter. 

---