Molecular dynamics nonbonded interactions

In an atomic level simulation, the bond stretch vibrations are usually the fastest motions in the molecular dynamics of biomolecules, so the evolution of the stretch vibration is taken as the reference propagator with the smallest time step. The nonbonded interactions, including van der Waals and electrostatic forces, are the slowest varying interactions, and a much larger time-step may be used. The bending, torsion and hydrogen-bonding forces are treated as intermediate time-scale interactions. 

Parallel molecular dynamics codes are distinguished by their methods of dividing the force evaluation workload among the processors (or nodes). The force evaluation is naturally divided into bonded terms, approximating the effects of covalent bonds and involving up to four nearby atoms, and pairwise nonbonded terms, which account for the electrostatic, dispersive, and electronic repulsion interactions between atoms that are not covalently bonded. The nonbonded forces involve interactions between all pairs of particles in the system and hence require time proportional to the square of the number of atoms. Even when neglected outside of a cutoff, nonbonded force evaluations represent the vast majority of work involved in a molecular dynamics simulation. 

Before running a molecular dynamics simulation with solvent and a molecular mechanics method, choose the appropriate dielectric constant. You specify the type and value of the dielectric constant in the Force Field Options dialog box. The dielectric constant defines the screening effect of solvent molecules on nonbonded (electrostatic) interactions. 

Features. GEMM is written in a host-independent manner and it has been run with an Apollo, a VAX, and a MicroVAX II as a host. GEMM can currently perform the following operations perform molecular dynamics, perform energy minimizations, compute the energy and forces for a structure, and update the nonbond list (nonbond lists are usually automatic for the other operations). In addition, a wide variety of I/O sequences are possible, such as what is needed for interactive modelling work. 

In Section 3.1., we shall show that the dynamic model leads to an unambiguous determination of the type of nonbonded interactions involved while the static model may lead to erroneous predictions as a result of an ambiguous definition of the nature of a nonbonded interaction. The superiority of the dynamic model is due to the fact that nonbonded interactions affect bonded interactions and, thus, the change in an overall overlap population rather than the change of a specific overlap population between nonbonded atoms or groups is the most appropriate index of a nonbonded interaction. Accordingly, we shall employ the dynamic model in all subsequent discussions of molecular structure, unless otherwise stated. 

The sizes of the dendrimers have been determined by calculating the molecular volumes, as defined by the van der Waals radii of the atoms, and by calculating the radii of gyration for several configurations of the dendrimers, as obtained from a molecular dynamics simulation at room temperature. The solvent influence on the calculated radii was estimated by scaling the nonbonded interactions between the atoms. Molecular volumes and average radii for ensembles of 500 conformations of the BAB-dendr-(NH2)D dendrimers have been collected in Table 26.2. 

This work is based on the molecular dynamic simulation of a monomer scale model corresponding to the affine network model of rubber elasticity.3 However, whereas the classic model has no nonbonded interactions, our model... 

Recently, detailed molecular pictures of the interfacial structure on the time and distance scales of the ion-crossing event, as well as of ion transfer dynamics, have been provided by Benjamin s molecular dynamics computer simulations [71, 75, 128, 136]. The system studied [71, 75, 136] included 343 water molecules and 108 1,2-dichloroethane molecules, which were separately equilibrated in two liquid slabs, and then brought into contact to form a box about 4 nm long and of cross-section 2.17 nmx2.17 nm. In a previous study [128], the dynamics of ion transfer were studied in a system including 256 polar and 256 nonpolar diatomic molecules. Solvent-solvent and ion-solvent interactions were described with standard potential functions, comprising coulombic and Lennard-Jones 6-12 pairwise potentials for electrostatic and nonbonded interactions, respectively. While in the first study [128] the intramolecular bond vibration of both polar and nonpolar solvent molecules was modeled as a harmonic oscillator, the next studies [71,75,136] used a more advanced model [137] for water and a four-atom model, with a united atom for each of two... 

Molecular dynamics are time-consuming because the nonbonded interactions scale as n where n is the number of atoms. To save time, one may implement the united atom approach, substituting some atomistic detail with an imaginary entity that represents the essential features of what has been substituted. For example, it is common to substitute methylene groups with an imaginary spherical atom with mass 14. Therefore a polyethylene chain would look like a chain of spherical atoms, appropriately rescaled, terminated by similar entities with mass = 15 for the methyl groups. 

The motions of proteins are usually simulated in aqueous solvent. The water molecules can be represented either explicitly or implicitly. To include water molecules explicitly implies more time-consuming calculations, because the interactions of each protein atom with the water atoms and the water molecules with each other are computed at each integration time step. The most expensive part of the energy and force calculations is the nonbonded interactions because these scale as 77 where N is the number of atoms in the system. Therefore, it is common to neglect nonbonded interactions between atoms separated by more than a defined cut-off ( 10 A). This cut-off is questionable for electrostatic interactions because of their 1/r dependence. Therefore, in molecular dynamics simulations, a Particle Mesh Ewald method is usually used to approximate the long-range electrostatic interactions (71, 72). 

Eastman, P., Pande, V.S. Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. J. Comput. Chem. 2010, 31,1268-72. 

Fig. 8-5. Rubredoxin on pyrophyllite. When proteins are placed into the interlayer space of a 2 1 clay mineral, the interactions of the protein with the mineral surface compete with intraprotein nonbonded interactions, (a) The crystal structure of rubredoxin taken from the Brookhaven Protein Data Bank is shown in the interlayer space of pyrophyllite, which has been artificially expanded to 5 nm. (b) During the course of NVT molecular dynamics simulation, end groups of the protein begin to interact with, and migrate along, the mineral surface, (c) When the system is then subjected to NPT molecular dynamics, the interlayer space collapses, compressing the protein from a diameter of 3.6 to 2,4 nm.

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