A 12 [Angstrom] cutoff distance was used to calculate short-range nonbonded interactions. The particle mesh Ewald (PME)  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
Molecular mechanics (MM) force fields rely on the combination of Coulomb and Lennard-Jones interactions to describe all nonbonded interactions
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).