Umbrella Sampling Simulation Service

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.

Analysis of umbrella sampling results.Figure 1. Umbrella sampling simulation.

Our simulation services

Project name Umbrella sampling simulation service
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

Our process of umbrella sampling simulation service:

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

Process of umbrella sampling simulation.Figure 2. Our process of umbrella sampling simulation service. (CD ComputaBio)

Features

  • Manipulating molecular dynamics.
  • Interactive molecular dynamics.
  • Visualization program for displaying, animating and analyzing biomolecular systems.

We provide a variety of molecular dynamics simulation service, but not limited to:

Umbrella sampling simulation service 1

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.

* For Research Use Only.

Inquiry

logo

CONTACT US

© 2021 CD ComputaBio. All rights reserved.