In a recent paper [S. Khrapak, Molecules 25, 3498 (2020)], the longitudinal and transverse sound velocities of conventional Lennard–Jones system at liquid–solid coexistence were calculated. It was shown that remain almost invariant along boundary lines their magnitudes are comparable with those repulsive soft-sphere hard-sphere models fluid–solid phase transition. This implies attraction does n...

Equilibrium configurations of rigid building blocks with multiple embedded interaction sites are investigated, as a coarse-grained approach for conformational sampling of protein structures with known secondary structure. First, hypothetical structures of asymmetric shapes, and pairs of rods composed of multiple interaction sites are considered. The rods are either disconnected or joined by a f...

In molecular mechanics, current generation potential energy functions provide a reasonably good compromise between accuracy and effectiveness. This paper firstly reviewed several most commonly used classical potential energy functions and their optimization methods used for energy minimization. To minimize a potential energy function, about 95% efforts are spent on the Lennard-Jones potential o...

In this study, the behavior of a one dimensional (1D) Lennard-Jones (LJ) system is simulated. As part of this research, a special purpose computer program was designed, coded, and tested. In both the model and the program calculations, energy and momentum are conserved. The modeling assumes constant pressure throughout each simulation, although several different pressures are modeled. The simul...

In this report some numerical results are presented for a special class of global optimization methods applied to molecular conformation problems. Following the results of a previously published method, in this report the authors show how some modifications to the basic structure of those algorithms enables us to obtain the optimal configuration for all clusters of Lennard-Jones atoms up to 80 ...

In this paper, two finite difference numerical schemes are proposed and analyzed for the droplet liquid film model with a singular Lennard--Jones energy potential involved. Both first second or...