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].

* Country or Region:

* Calculation simulation needed:
(please describe in detail what you want to calculate, or the research purpose you want to achieve through the calculation)

* Expected results:
(please fill in the details if you have expected results or have corresponding experimental results)

* The structure of the system to be calculated:
(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)

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