Calculation of local strain tensors based on the relative motion of neighboring particles of a solvated 5-dimensional peptide

Abstract

In this research paper, a peptide was considered, namely, the ratio of points of volumetric deformationfrom shear deformation was considered and the dependence of the output strain tensor on theoutput tension tensor was investigated. In this paper, the deformation in 2000 steps of the peptidewas modeled with the calculation of the volumetric deformation from shear deformation and thecalculation of local tensors was investigated. 1466 per simulated step was considered in more depth,since it was during the study at this simulated step that the particles and particles of the "neighbors"of the peptide showed the maximum peak of activity. The article considered two software packages.A freely distributed LAMMPS package for performing system modeling on multiprocessor computingsystems, which implements the molecular dynamics method at its core, and in which the behavior ofparticles of a solvated 5-dimensional peptide was formed and implemented. And the freely distributed,second OVITO software package, which was used to visualize and recognize the deformation of thepeptide. Namely, the OVITO package made it possible to recognize and calculate experimental datain the simulated atomic system, which are reflected in this scientific work.