Then, inspired by the Lennard-Jones potential, we define a data-driven social potential function and apply the resultant force to a real e-mail communication network in a course of a molecular simulation, with network nodes taking on the role of interacting particles. We discuss all steps of ...
This approach, however, does not capture the observed changes in the dielectric response of the junctions directly, and, of course, it does not explicitly account for the local changes in the electrostatic potential profile induced by X observed in the DFT calculations; these effects are ...
MD simulation protocol: Using the GROMACS 5.1 package20, MD simulations were performed with the AMBER14SB force field for the protein21and derived parameters for phosphoserine22. The systems were explicitly solvated using cubic water boxes with TIP3P water23, under periodic boundary conditions. The ...
Diffusion of ferrous ion was observed during the course of molecular dynamic simulation which corresponded to the postulated mechanism of iron transport. Further, the dock scores correlated well with relative bioavailabilities of the iron compounds. The study confirmed the efficacy of the in silico ...
During the course of a molecular dynamics simulation, the electrostatic and van der Waals forces produced by ligand atoms are turned down gradually enough to avoid undesirable artifacts. Eventually, the ligand is no longer able to interact with the protein or solvent. For all practical purposes, ...
Also short simulation time-scales will be associated with kinetic effects. However kinetic effects are also present in experiment (although to a lesser degree), as discussed previously [11], and physiological surfactant function is also dynamic in nature, and as such is subject to kinetic factors...
The effect of the tacticity of poly methyl methacrylate (PMMA) on the morphology of free volume in PMMA membranes was studied by using a molecular dynamics simulation technique. The chain flexibility, chain interaction, end-to-end distance of a chain and the time course of the free volume vari...
Molecular Dynamics Simulation and Computational Two-:分子动力学模拟和计算两—计算,模拟,评价,and,And,分子动力学,AND,计算分子,百度快照 文档格式: .pdf 文档大小: 436.39K 文档页数: 7页 顶/踩数: 0/0 收藏人数: 0 评论次数: 0 文档热度:
We performed the simulation of the membrane-water system in three stages. During the first stage, we applied restraints on all non-solvent heavy atoms; we then energy-minimized the system for several hundred thousand steps using steepest-descent first and then conjugated gradient. Afterwards, we ...
the prepared systems were fully energy-minimized and subsequently equilibrated. The temperature in equilibration process was gradually increased from 10 to 298.15 K. The MD simulation was run for ~20 ns with the time step of 2 fs and the cutoff value for the non-bond interactions of ...