Stochastic boundary molecular dynamics simulations

To explore these effects more thoroughly, results are presented from stochastic boundary molecular dynamics simulations of the active-site cleft of lysozyme in the presence of aqueous solvent and in vacuum.108 The simulation... 

The correlation function, <-P2[am(0) ( )]>. provides a measure of the internal motions of particular residues in the protein.324 333 Figure 46 shows the results obtained for Trp-62 and Trp-63 from the stochastic boundary molecular dynamics simulations of lysozyme used to analyze the displacement and velocity autocorrelation functions. The net influence of the solvent for both Trp-62 and Trp-63 is to cause a slower decay in the anisotropy than occurs in vacuum. In vacuum, the anisotropy decays to a plateau value of 0.36 to 0.37 (relative to the initial value of 0.4) for both residues within a picosecond. In solution there is an initial rapid decay, corresponding to that found in vacuum, followed by a slower decay (without reaching a plateau value) that continues beyond the period (10 ps) over which the correlation function is ex-... 

Field Stochastic Boundary Molecular Dynamics Simulation of a Phospholipid in a Membrane. 

For an understanding of protein-solvent interactions it is necessary to explore the modifications of the dynamics and structure of the surrounding water induced by the presence of the biopolymer. The theoretical methods best suited for this purpose are conventional molecular dynamics with periodic boundary conditions and stochastic boundary molecular dynamics techniques, both of which treat the solvent explicitly (Chapt. IV.B and C). We focus on the results of simulations concerned with the dynamics and structure of water in the vicinity of a protein both on a global level (i.e., averages over all solvation sites) and on a local level (i.e., the solvent dynamics and structure in the neighborhood of specific protein atoms). The methods of analysis are analogous to those commonly employed in the determination of the structure and dynamics of water around small solute molecules.163 In particular, we make use of the conditional protein solute -water radial distribution function,... 

Other dynamic simulations commonly used are Brownian dynamics- " and stochastic boundary molecular dynamics." These techniques are suitable when interest is limited to a small portion of a large system and the molecular details of the rest of the system are not of concern. Under such situations, MD will be an inefficient choice. For example, if the effect of a solvent on the dynamics of a solute molecule can be obtained by a suitable choice of parameters in the potential function, one can study the dynamics in more detail for longer times. In Brownian dynamics, the forces acting on a solute molecule have a component from intramolecular interactions in the solute and/or any external field, a component arising from the solvent friction, and a third random component to model the thermal fluctuations of the solvent molecules ... 

A. Briinger, C. L. Brooks, III, and M. Karpins. Stochastic boundary conditions for molecular dynamics simulations of ST2 water. Chem. Phys. Lett., 105 495-500, 1982. 

To illustrate the solvent effect on the average structure of a protein, we describe results obtained from conventional molecular dynamics simulations with periodic boundary conditions.92,193 This method is well suited for a study of the global features of the structure for which other approaches, such as stochastic boundary simulation methods, would not be appropriate. We consider the bovine pancreatic trypsin inhibitor (BPTI) in solution and in a crystalline environment. A simulation was carried out for a period of 25 ps in the presence of a bath of about 2500 van der Waals particles with a radius and well depth corresponding to that of the oxygen atom in ST2 water.193 The crystal simulation made use of a static crystal environment arising from the surrounding protein molecules in the absence of solvent. These studies, which were the first application of simulation methods to determine the effect of the environment on a protein, used simplified representations of the surround-... 

Any of the methods used in classical Monte Carlo and molecular dynamics simulations may be borrowed in the combined QM/MM approach. However, the use of a finite system in condensed phase simulations is always a severe approximation, even when appropriate periodic or stochastic boundary conditions are employed. A further complication is the use of potential function truncation schemes, particular in ionic aqueous solutions where the long-range Coulombic interactions are significant beyond the cutoff distance.Thus, it is alluring to embed a continuum reaction field model in the quantum mechanical calculations in addition to the explicit solute—solvent interaaions to include the dielectric effect beyond the cutoff distance. - uch an onion shell arrangement has been used in spherical systems, whereas Lee and Warshel introduced an innovative local reaction field method for evaluation of long-... 

Kantorovich, L., 8cRompotis, N. (2008). Generalized Langevin equation for solids. II. Stochastic boundary conditions for nonequilibrium molecular dynamics simulations. Physical Review B, 78, 094305. 

In the following, we briefly describe the techniques commonly employed in computer simulation studies of lipid assemblies (and of other biomole-cules " ), namely, Monte Carlo (MC) and dynamic simulations such as molecular dynamics (MD), Brownian dynamics and stochastic boundary mo-... 

MARESCHAL - In the Benard problem, the thermal boundaries are simulated along the ways developped in non-equilibrium molecular dynamics, using stochastic boundary conditions (see G. Ciccotti). The boundary layer does not extend over more than a mean free path in the system and can hardly be seen in our measurements. 

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