Discontinuous molecular dynamics

Keywords Coarse-grained model Protein-protein interactions Discontinuous molecular dynamics Square-well potential Osmotic second virial coefficient... 

Here, we report the development of a two-bead-per-residue protein model that can be used with discontinuous molecular dynamics (DMD) simulations to investigate protein-protein interactions in a multi-protein system. We expect that this new model will allow us to simulate multi-protein systems on longer timescales than what has heretofore been achievable, helping us to deepen our understanding of processes such as protein crystallization [1], protein recognition [2], and protein purification [3]. 

Discontinuous molecular dynamics (DMD) simulations can be used to investigate large systems efficiently with moderate computational resources. DMD simulations were designed to be applicable to systems that interact via discontinuous potentials (square-well/square-shoulder and hard-sphere). They proceed by analytically calculating the next collision time. Several papers [26-28] describe the details of DMD simulations. The algorithm complexity of DMD simulations is O (Mog N). (One paper by Paul [29] even claims a realization of the DMD method... 

Recently, Strickland et have used computer simulations to examine situations in which the modified monomeric unit exhibited lower, identical, or greater solubility when compared with the original unmodified monomer. They presented the results of discontinuous molecular dynamics (also referred to as event-driven molecular dynamics) simulations of polymer-analogous reactions with special focus on the case in which the chemically modified monomers had different solubility than the parent homopolymer. A system of polymer... 

In their simulations, Strickland et al ° employed discontinuous molecular dynamics to study the coloring process in macromolecular tethers made of various lengths. Specifically, they explored the effect of the grafting density of the parent polymer and the interplay between the solubilities of the unmodified and modified segments along the polymeric grafts on the comonomer distribution in designed copolymers. 

When the cutoff is sharp, discontinuities in the forces and resultant loss of con servation of energy m molecular dynamics calcnla-tionscan result.To minimi/e edge effects of a cu toff, often theciit-off IS implemented with a switching or shifting function to allow the interactions to go smoothly to /ero. 

The interface between the droplet and the gas is not discontinuous the average molecular density decreases over a narrow region from the liquid side to the vapor. When the size of the droplet becomes sufhctently small compared with the thickness of the transition layer, the use of classical thermodynamics and the bulk surface tension become inaccurate the Kelvin relation and Laplace formula no longer apply. This effect has been studied by molecular dynamics calculations of the behavior of liquid droplets composed of 41 to 2(X)4 molecules that interact through a Lennard-Jones (LI) intermolecular potential (Thomp.son et al., 1984). The results of this analysis are shown in Fig. 9.5, in which the nondimensional pressure difference between the drop interior and the surrounding vapor (Pd — p)rr / ij is... 

These equations all use distances and energies in reduced units and the functional form is designed to go to zero without discontinuities at the cutoff distance r = a. There are seven parameters (A, B, p, q, a. A, 7), which were determined by a search procedure, with care being taken to ensure that the diamond structure was the most stable periodic arrangement and that the melting point and liquid structure (as determined by molecular dynamics simulations) were in reasonable agreement with experiment. The three-body term is... 

If a cutoff is abruptly applied at a particular interatomic distance, this discontinuity can cause problems in energy minimization and molecular-dynamics calculations. To avoid this, one can use a cutoff that makes the nonbonded interactions go to zero gradually over a distance of, say, 1 A. This is done using what is called a switching function. 

Smith, S.W., Hall, C.K., Freeman, B.D. Molecular dynamics for polymeric fluids using discontinuous potentials. J. Comput. Phys. 134, 16-30 (1997)... 

Generally, in molecular dynamics a computer is used to solve numerically the classical equations of motion for an assembly of N (usually several hundred) interacting particles in a box of side L. We shall restrict our attention to those cases where the interaction can be specified by a pairwise-additive, continuous potential function. Because discontinuous potentials require very different techniques, they are discussed in Chapter 1. The output of the... 

A common Molecular Dynamics approach in studies of confined systems at fixed chemical potential employs an isobaric, bulk-like bath surrounding the confinement. The conditions inside a field-exposed confinement (e.g., inside a capacitor) should therefore be close to (p, V, T) ones of GCMC cases [66, 68], suggesting similar electrostriction behavior. Occurrence of a field-induced expulsion of water has, however, been reported in a Molecular Dynamics study of this kind [57]. To secure proper barostat performance under strongly nonuniform and anisotropic pressure fields, and to account for the discontinuity between field/no... 

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