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Molecular Dynamics Simulation


What Is Molecular Dynamics Simulation?

As a multi-body simulation technique, molecular dynamics simulation method mainly relies on computers to simulate the movement of molecules and atomic systems. The behavior of the system over time can be investigated from a dynamic point of view by simulating the state of motion of molecules and atoms in a certain period of time. The trajectories of molecules and atoms can be obtained by numerically solving the Newtonian equation of motion, and the potential energy can usually be calculated from the potential energy function of the interaction between molecules and the force field of molecular mechanics. In addition, molecular dynamics simulation is the closest simulation method to experimental conditions in molecular simulation. Scientists therefore use it to study the microscopic evolution process of the system and investigate the mechanism from the atomic level.

Application of Molecular Dynamics Simulation in Drug Design

  • Study the properties of different proteins
  • Study the mechanism of ligand-receptor binding
  • Study the interaction between protein and membrane (lipid force field)
  • Study the mechanism of protein folding

Model of M1 structure and molecular dynamics simulation (MDS) of full-length M1 in solution.Figure 1. Model of M1 structure and molecular dynamics simulation (MDS) of full-length M1 in solution. (Hoefer, C.T; et al. 2018)

Our MD Simulation Services

With the deepening of quantum chemistry research and the improvement of computing software, they play an important role in the process of scientific research and chemistry teaching. We apply multiple quantum chemistry computing software to identify commercially available lead-like and drug-like compounds simulate for novel drug design. To make it easier and better for researchers, Alfa Chemistry provides practical molecular dynamics simulation in a competitive fashion. We have prepared the most convenient services for you.

Binding free energy calculation with MM/PB(GB)SA

Molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) and molecular mechanics generalized Born surface area (MM/GBSA) have been widely used in biomolecular studies such as protein folding, protein-ligand binding, protein-protein interaction, etc. At Alfa Chemistry, we use this accurate scoring functions of molecular docking to predict the binding free energy.

Cluster analysis

Cluster analysis is a powerful method for determining structure populations in molecular dynamics simulations. Our groups provide partitional clustering and agglomerative hierarchical clustering to study the polypeptides folding. We are capable of performing cluster analysis on the different conformations of proteins. Moreover, our scientists offer additional cluster evaluation services before carrying out cluster analysis.

Nonpolar solvation energy calculation with MM/PB(GB)SA

We calculate the nonpolar solvation energy using the solvent-accessible surface area method. In order to obtain the prediction which is in an excellent agreement with experimental data, our experts have modified the GB/SA model and optimized a series of factors that can affect the calculation of MM/PB(GB)SA.

Polar solvation energy and entropy calculation with MM/PB(GB)SA

As an important part of the binding energy, the polar solvation energy comes from the electrostatic interaction between the solute and the solvent molecules. For different studied system, Alfa Chemistry provides PB equation or GB approach to perform the polar solvation energy calculation. Moreover, the contribution of the entropy of the gas phase is calculated according to the MM method in the MM-PBSA method.

Principal component analysis (PCA)

Principal component analysis is a useful multidimensional data analysis technique that has been commonly applied in the MD simulation. PCA can significantly reduce the complexity of calculations by expressing molecular information more simply and effectively. We have established a well-designed PCA process using either Cartesian coordinates or backbone dihedral angles. Our PCA results can help to analyze important motions in biomolecules or discriminate relevant conformational changes in proteins.

Targeted molecular dynamics (TMD) simulation

TMD simulation method, established on the basis of MD simulation technology, is able to simulate more elaborate conformational changes in proteins. Alfa Chemistry supports a restricted perturbation-targeted molecular dynamics method as well as dissipation-corrected targeted molecular dynamics simulations. Our scientists use TMD simulation to model the pathways, simulate the conformational transition simulation, and explore ligand binding reaction coordinates.

Umbrella sampling simulation

Our groups have developed a umbrella sampling simulation method combined with potential of mean force analysis to conduct the binding energy calculation. Moreover, our umbrella sampling simulation is available to predict the protein-ligand affinity and probe the energy barrier of the folding pathways.

Our Advantages

  • Flexible and advanced computational methods
  • High-performance computer server
  • Professional drug design team
  • Personalized and customized innovative scientific research services
  • Cost-efficient and time-saving

Our molecular dynamics simulation services remarkably reduce the cost, promote further experiments, and enhance the understanding of catalytic reactions for customers worldwide. Our personalized and all-around services will satisfy your innovative study demands. If you are interested in our services, please don't hesitate to contact us. We are glad to cooperate with you and witness your success!


  • Narouz, M. R.; et al. N-heterocyclic carbene-functionalized magic-number gold nanoclusters. Nature Chemistry. 2019.

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