Protheragen has extensive experience in the field of molecular dynamics simulation (MD) services. Over the years, our computational chemist have provided many simulation services to hundreds of pharmaceutical and biotechnology companies. MD simulation is a set of molecular simulation methods, which is a powerful tool for studying the interaction of biological macromolecules and chemical compounds, and condensed matter systems. Through molecular dynamics simulation, researchers can obtain the motion trajectory of the atoms in the system and observe various microscopic details of the atomic motion process. Through the dynamic simulation of the research system, we can understand the movement and biological functions of biological macromolecules, the interaction mechanism between protein and small molecules, and the self-assembly process of nanomaterial molecules at the molecular level. Molecular dynamics simulation is a powerful supplement to theoretical calculations and experimental methods, and is widely used in the fields of physics, chemistry, materials science, and biomedicine.
Under the premise of ignoring the quantum effect of atomic nuclei and the adiabatic approximation of Born-Oppenheimer, molecular dynamics relies on Newtonian mechanics to simulate the motion of molecular systems, and samples are drawn from systems composed of different states of molecular systems, calculate the thermodynamic quantities and other macroscopic properties of the system. In molecular dynamics simulation, empirical potential is generally used to replace the interaction potential between atoms, such as Lennard-Jones potential, Mores potential, EAM atom insertion potential, F-S many-body potential.
Figure 1. Process of molecular dynamics simulations.
Protheragen currently has molecular dynamics software such as AMBER, GROMACS and NAMD. Relying on the platform's computing resources, it can perform dynamic simulations with a time span of 100ns in a short time. By analyzing the clustering of the simulated trajectory, the relatively stable configuration of each state between the molecules can be obtained, and the mechanism of the interaction between the molecules can be identified by analyzing the interaction mode and the interaction energy between the molecules.
|Project name||Molecular Dynamics Simulation Service|
|Cycle||Depends on the time you need to simulate and the time required for the system to reach equilibrium.|
|Product delivery mode||The simulation results provide you with the raw data and analysis results of molecular dynamics.|
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