Coarse-grained Dynamics Simulations

Coarse-grained simulation aims to use its coarse-grained (simplified) representation to simulate the behavior of complex systems. Coarse-grained models are widely used for molecular modeling of biomolecules of various granularity levels. Various coarse-grained models have been proposed. They are usually dedicated to the computational modeling of specific molecules: proteins, nucleic acids, lipid membranes, carbohydrates or water. Coarse-grained models have found practical applications in molecular dynamics simulations.

Common coarse-grained model.Figure 1. Coarse graining model of common molecules.

Difference between coarse-grained simulation and all-atom dynamics simulation

All-atom simulation and coarse-grained simulation.

  • In molecular dynamics simulations, the simulation with atoms as the basic unit is called an all-atom simulation, and the corresponding model is called an all-atom model.
  • The full-atomic simulation can simulate about 102 to 106 atoms, and the simulation time scale is about nanoseconds.
  • All-atomic simulation mainly studies the structural and functional changes of a single biomolecule under different physiological conditions.
  • However, intracellular interaction processes (such as protein-protein docking, ligand binding site conformational changes, macromolecular folding, etc.) usually involve a large number of different types of biomolecules and collective movement of biomolecules, usually lasting more than a few microseconds to milliseconds level.
  • Traditional all-atom simulation is difficult to achieve. Therefore, by simplifying the details of all-atom simulation to reduce the degree of freedom of the simulation system, a long-term large-scale simulation method-coarse grain (CG) simulation method was created.

Our simulation services

Project name Coarse-grained dynamics simulations
Samples requriements The initial structure of PDB ID, etc.
Detection cycle Depends on the time you need to simulate.
Service including We provide you with raw data and calculation result analysis service.
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Coarse-grained dynamics simulations 1

The implementation of coarse-grained simulation mainly involves four aspects:

  • The construction of coarse-grained beads.
  • The interaction and parameterization of beads.
  • The establishment and optimization of coarse-grained simulation system.
  • The handling of special problems in the simulation.

Coarse-grained dynamics simulations 2

We can offer coarse-grained simulation service but not limited to:

  • Self-assembly of lipid molecules.
  • Interaction between lipid bilayer and protein.
  • Membrane protein accumulation on lipid bilayer.
  • Residue-Based Coarse Graining.
  • Shape-Based Coarse Graining.

CD ComputaBio offers a corresponding coarse-grained dynamic simulation. Our molecular dynamics simulations provide accurate approximations of real molecular behaviors, and have proven to be very useful in understanding the biochemical basis of physiological events at different stages of drug development, even in different fields such as materials science. Our team of experts can provide up to one millisecond of simulation time for the system you choose, so you do not have to worry about technical issues. We can also analyze these results for you. The CD ComputaBio team has been working in this field for more than ten years and has published his findings in top scientific journals.

We provide a variety of molecular dynamics simulation service, but not limited to:

* It should be noted that our service is only used for research, not for clinical use.

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