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

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from molecular
docking to kinetic
simulation
High performance
computer servers
Professional
molecular simulation
and drug design
team
Diversified analyses
available
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price advantage
High standard of
data privacy
management

If you have any questions, please do not hesitate to contact us via email sales@MedChemExpress.com.

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* Calculation simulation needed:
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* 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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Compound
Screening Libraries

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Compound Customization

Specific Compounds
Quantities
Plate Map
Concentration
Form (Solid or Solution)
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