Molecular Dynamics Simulation

Molecular dynamics is a computer simulation method based on Newtonian mechanics and integrating various disciplines such as physics, mathematics and chemistry, which is used to study the motions and interactions of molecular systems and to predict the behavior and structural properties of molecular systems. Through computer molecular simulation, researchers are able to understand the motion and biological functions of biomolecules and protein-small molecule interaction mechanisms at the molecular level. Currently, MD has been widely used in the fields of biomedicine, physics, chemistry and materials science, and is a powerful complement to theoretical calculations and experiments.

Obtaining Molecular
Structure Setting Main
Parameter Molecular Dynamics
Simulation Data Analysis Giving the corresponding
molecular force field Setting of box size and
pH values Optimizing the system
energy

Figure 1. Diagram of molecular dynamics simulation (Food Chem. 2023 Mar 30;405(Pt A):134824.)

Analysis Items

  • • Skeleton fluctuation: RMSD, RMSF
  • • Interaction analysis: hydrogen bond network, salt bridge, Contact-Map, etc.
  • • Conformational transformation: PCA, Energy-landscape plotting
  • • Hot residues: Alanine-scanning, Energy-decomposition
  • • Conformational sampling: cluster analysis, dominant conformation identification
  • • Binding free energy: MM-PBSA, TI, FEP
  • • Physicochemical properties: Energy, volume, pressure, temperature, density monitoring

Service Advantages

  • One-stop service
    from molecular
    docking to kinetic
    simulation

  • High performance
    computer servers

  • Professional
    molecular simulation
    and drug design
    team

  • Diversified analyses
    available

  • Competitive
    price advantage

  • High standard of
    data privacy
    management

If you have any questions, please do not hesitate to contact us via email [email protected].

Product Customization

  • (please describe in detail what you want to calculate, or the research purpose you want to achieve through the calculation)

  • (please fill in the details if you have expected results or have corresponding experimental results)

  • (for periodic systems such as crystals, please provide the corresponding cif file; for protein systems, please provide the pdb file or sequence; for molecular systems, please provide the cdx file exported by chemdraw or the corresponding molecular structure formula. Attachments can be provided separately)