Lipid Molecular Dynamics Simulation Service

One of the major challenges in understanding biophysics is to understand the basic principles of controlling lipid bilayer mixtures. Lipid bilayers or membranes control and mediate various biologically related processes at the cellular level. In addition to cell membranes, lipid membranes also exist in various man-made applications, such as liposomes (and many natural entities, such as lipoproteins) used in new drug delivery technologies. The various situations in which lipid bilayers play an important role do make people are fascinated. However, although experimental methods are the cornerstone of membrane research, it is often difficult or even impossible to obtain a thorough understanding of the phenomena that occur in the lipid bilayer through experiments alone. Therefore, atomic computer simulation technology ( For example, classical molecular dynamics (MD) has become a standard tool for studying biological membrane systems at the molecular level. CD ComputaBio provides you with professional lipid molecular dynamics simulation services.

Figure 1. Lipid molecular dynamics simulations.

Overall solutions

CD ComputaBio has developed a novel scheme for comparing the structural properties of the lipid bilayer determined by simulation with the bilayer properties determined by diffraction experiments, which allows rigorous testing of the ability of molecular dynamics simulation to reproduce experimental data.

• Diffraction-based membrane density constraints and membrane peptide molecular dynamics simulation
  We recently discovered that the current molecular dynamics (MD) atomic force field cannot yet produce a lipid bilayer structure consistent with the experimentally determined structure within the experimental error range. Due to the many advantages of experimentally verified simulations, we developed a new film MD simulation constraint method using experimental diffraction data.
• Study on the size effect of finite system in lipid bilayer molecular dynamics simulation
  In the absence of external stress, the surface tension of the lipid film disappears in an equilibrium state, and the film shows long-wavelength fluctuations, which can be said to be elastic deformation (mainly with tension). These long-wavelength fluctuations are usually suppressed in the molecular dynamics simulation of the membrane. As a result, the limited system size effect in molecular dynamics over the past few years, some people believe that it is necessary to simulate the small diaphragm under tension to correctly simulate the tension-free state of the macroscopic membrane. Our latest hardware and software advancements make it possible to simulate a larger all-atom system, which allows us to directly solve the problem of whether the current smaller simulation size of the membrane will affect its physical properties compared to the actual macro double-layer system .

Our Features

• Our lipid molecular dynamics simulation service can study the solvent effect of aqueous or organic solvents.
• Our lipid molecular dynamics simulation service supports various force fields, such as CHARMM, AMBER and OPLS.
• We can simulate long-term high-performance programs (GPU acceleration) and provide free energy calculations (binding, solvation, interaction).
• We can provide visualization programs for display, animation and analysis of biomolecular systems.
• Our molecular dynamics simulation saves a lot of labor costs, the calculation cycle is short, the speed is fast, the required funds are far less than the biological or chemical experiments, and the calculation accuracy is high. If you have any needs in this regard, please feel free to contact us.