In umbrella sampling, the energy pattern is "flattened" by adding artificial "umbrella" potential that should "mirror" and thus eliminate practical obstacles. Umbrella sampling can speed up sampling by "flattening" hills and ridges, thus preventing MD from accessing certain states. Therefore, the umbrella potential involves only a few (usually one to three) degrees of freedom, often called collective variables or reaction coordinates. When the system "accesses" all values of the set variable multiple times (ie, the number of times required to make accurate and unbiased calculations of state probabilities), the system sampling is considered complete.
Figure 1. Illustration of umbrella sampling simulations on induced minor groove opening in two DNA sequences (Curuksu J, et al., 2015)
Project name | Umbrella sampling simulation service |
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Samples requirement | The initial structure of PDB ID, etc. |
Timeline | Depends on the time you need to simulate. |
Deliverables | We provide you with raw data and calculation result analysis service. |
Price | Inquiry |
Step1 |
Prepare the topology file |
Step2 |
Define the unit cell |
Step3 |
Add solvents and ions |
Step4 |
Generated configuration |
Step5 |
Generated configuration |
Step6 |
Add solvents and ions |
Step7 |
Data analysis |
Figure 2. Our process of umbrella sampling simulation service. (CD ComputaBio)
CD ComputaBio can provide you with umbrella sampling simulation technology. Umbrella sampling is a very popular technique that can be used to calculate the average force (PMF) to study the protein binding-unbinding process. Later, one can also extract binding free energy from the obtained PMF. The CD ComputaBio team has been working in this field for more than ten years and has published his findings in top scientific journals.
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