Molecular Dynamics Simulation Service

Molecular Dynamics (MD) simulation is a set of molecular simulation methods and a powerful tool for studying condensed matter systems. Through molecular dynamics simulations, researchers get the trajectory of the atoms in the system, and can observe various microscopic details of the process of atom movement. The movement and biological function of biological macromolecules, the interaction mechanism between protein and small molecules, and the self-assembly process of nanomaterial molecules at the molecular level can all be understood. Molecular dynamics simulation is a powerful supplement to theoretical calculations and experimental methods, and is widely used in the fields of physics, chemistry, material science, and biomedicine.

Molecular dynamicsFigure 1. Molecular dynamics simulation. (CD ComputaBio)

Our simulation services

Project name Molecular dynamics simulation service
Samples requirement Protein, enzyme, lipid, membrane protein,petide., etc.
Timeline 3-5 days.
Deliverables We provide you with raw data and calculation result analysis service.
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Our simulation service process

Determine the starting configuration

The first step in molecular dynamics simulation is to determine the initial configuration. The lower energy initial configuration is the basis of molecular simulation.

Enter equilibrium phase

The molecules identified in the previous step form an equilibrium phase, and its configuration, temperature, and other parameters are monitored when the equilibrium phase is constructed.

Enter the production phase

After entering the production stage, the molecules and atoms in the system begin to move according to the initial speed.

Calculation results

Use the various states of the sampled system to calculate the potential energy of the system at that time, and then calculate the configuration integral.

Molecular dynamics simulation service

Our advantages

  • Mature and reliable molecular simulation platform: rich project experience, participate in major projects and release advanced cooperation results.
  • Based on high-quality data analysis, the analysis contents and methods of pre-research and verification are indeed mature and feasible.

Our molecular dynamics simulation services

Applications of Molecular dynamics simulation service

CD ComputaBio provides corresponding molecular dynamics simulation services. Our molecular dynamics simulations provide accurate approximations of the behavior of real molecules and have proven to be very useful for understanding the different stages of drug development. We can also analyze these results for you. If you are interested in our services, please contact us for more detailed information.

Molecular Dynamics Simulation Service FAQs

    • Q: What are the conventional molecular dynamics simulations and methods?
      • A: We can offer the following methods:

        Study of the interaction mechanisms of ligand-receptor complex systems: interaction patterns, induced fit effects, protein backbone motions.
        Predicting the binding free energy of active small molecules (in relation to Ki, IC50) to elucidate the mechanism or to guide structural modification.
        Optimization of protein structures, e.g. structural optimization of structures obtained from homology modelling.

        Other advanced methods we offer:

        Molecular dynamics of membrane proteins.
        Stretching molecular dynamics (SMD).
        Copy exchange molecular dynamics (REMD).
        Targeted molecular dynamics (TMD).
        Micro-motion elastic band (NEB) calculations.
    • Q: What are the MD Result analysis services you can provide?
      • A: We can offer the following result analysis services according to your scientific needs:

        Backbone fluctuations: RMSD, RMSF.
        Interactions: hydrogen bonding, salt bridges, angles, dihedral angles, hydration, interaction spectra.
        Binding free energy: MM/PB(GB)SA.
        Conformational sampling: clustering, PCA, simple normal mode analysis, secondary structure analysis, potential energy surface scanning, dominant conformation identification.
        QM/MM
        Study of enzyme catalytic mechanisms, often including transition state courses.
        Proton transfer, charge migration reaction processes.
        Induced luminescence mechanism.
    • Q: How to place an order for simulation calculation?
      • A: If the calculation demand is clear, you can directly choose the corresponding project on the CD ComputaBio website to make an appointment, and you need to fill in the specific calculation materials and calculation requirements when making an appointment. If you are not sure of the calculation content, you can contact the staff directly for demand communication.

    • Q: What is the scope of services for the simulation calculation project?
      • A: We provide the required calculation methods, data and graphics of the calculation results, and answers to questions about the calculation results after the calculation is completed. Proper answers can be provided for the simulation calculation questions in the article reply comments. If additional calculations are needed after the return of the article, additional charges are required.

    • Q: What if the calculation results do not match with expectations?
      • A: The scientific computing service is a process of exploration, in which there are uncertainties. The service provider is responsible for the data obtained from theoretical calculations, but we do not guarantee that the theoretical data will be exactly the same as the expected results. If necessary, the model can be adjusted appropriately, and if the adjustment process increases the calculation or large-scale recalculation, the calculation cost will be increased, and the price will be negotiated separately. There is uncertainty in the simulation calculation, and we are responsible for the correctness of the calculation process. Please understand that software, machine time and labor cost will be consumed after the calculation starts, so if the calculation is cancelled in the middle of the process, the corresponding fee will be charged.

* For Research Use Only.
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