At CD ComputaBio, we specialize in providing cutting-edge computational solutions for molecular dynamics simulations. One of our key offerings is the umbrella sampling molecular dynamics simulation service. Through this service, we enable researchers and organizations to gain valuable insights into the behavior of complex biological systems at the molecular level. Our team of experienced scientists and computational experts is dedicated to delivering high-quality simulations tailored to meet the specific needs of our clients.
Umbrella Sampling is a powerful technique used in molecular dynamics simulations to study the free energy landscape of biomolecular systems. By applying an external restraining potential, Umbrella Sampling allows researchers to explore the energetically unfavorable transitions that might occur during regular simulations. This method is particularly useful in investigating processes such as protein-ligand binding, protein conformational changes, and protein-protein interactions.
System Setup
Our experts work closely with clients to define the system of interest and set up the necessary parameters for the Umbrella Sampling simulation. This includes defining the collective variables, selecting suitable force fields, and configuring the simulation environment.
Simulation Protocol Development
We develop customized simulation protocols tailored to the specific research objectives of our clients. Our team ensures optimal sampling efficiency and accuracy by carefully designing the umbrella sampling windows and defining the biasing potentials.
Data Generation and Analysis
We conduct extensive molecular dynamics simulations to generate large datasets capturing the dynamics of the system under study. Our analysis includes the calculation of free energy profiles, potential of mean force (PMF) calculations, and exploration of key transition states.
| Service Tails | Descriptions |
|---|---|
| System | Send us the biomolecular system of interest, including proteins, nucleic acids, ligands, and solvent molecules. |
| Biasing Potentials | Definition of the biasing potentials for each window to sample the desired region of the free energy landscape. |
| Reaction Coordinate | Specification of the reaction coordinate along which the Umbrella Sampling windows will be defined. |
| Simulation Protocol | Details of the simulation parameters, such as temperature, pressure, integration time step, and simulation length. |
| Product Delivery Mode | The simulation results provide you with the raw data and analysis results of umbrella sampling simulation. |
CD ComputaBio stands as a beacon of excellence in the field of umbrella sampling molecular dynamic simulations, offering unparalleled expertise, state-of-the-art infrastructure, and customized solutions to meet the diverse needs of our clients. Whether you are exploring rare events, mapping free energy landscapes, or studying conformational dynamics, our service is designed to elevate your research to new heights. If you are interested in our services or have any questions, please feel free to contact us.
Services
Related Services: