A 12 [Angstrom] cutoff distance was used to calculate short-range nonbonded interactions. The particle mesh Ewald (PME) [32] method was used to calculate long-range electrostatic interactions.
It revealed that nonbonded interactions are a significant driving force in biomolecular interactions and stability.
Recent studies suggest that covalent interactions are informative when combined with
nonbonded interactions [33, 34].
Molecular mechanics (MM) force fields rely on the combination of Coulomb and Lennard-Jones interactions to describe all
nonbonded interactions [18].
Figueroa-Villar, "Influence of
nonbonded interactions in the kinetics of formation of chalcogenol esters from chalcogenoacetylenes," International Journal of Quantum Chemistry, vol.
Periodic boundary conditions were imposed with a 1.0 nm cutoff for
nonbonded interactions. Long-range electrostatic corrections were modeled by the particle mesh Ewald technique [27, 28].
The third term containing [q.sub.i, k] represents the contribution to potential energy due to
nonbonded interactions. Primed quantities are introduced as internal tensions.
This new server reduces processing time of molecular dynamics (*1) simulation with a dedicated computation board "MD Engine(R)"(*2) that processes time-consuming computation, nonbonded interactions at high speed.
Dedicated computation board for high-speed computations of nonbonded interactions
Simulation time has been dramatically reduced by an embedded "MD Engine(R)," a dedicated computation board for high-speed computation of nonbonded interactions such as coulomb force and intermolecular force that account for more than 99% in many cases of molecular dynamics simulation.
H chain of motavizumab formed three hydrogen bonds and
nonbonded interaction whereas no hydrogen bond was found when motavizumab interacted with L chain of fusion protein (Figure 5).
