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.

Illustration of umbrella sampling simulations on induced minor groove opening in two DNA sequencesFigure 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
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:


Prepare the topology file


Define the unit cell


Add solvents and ions


Generated configuration


Generated configuration


Add solvents and ions


Data analysis

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


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

Our molecular dynamics simulation services

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.


  1. 1.Curuksu J., Kannan S., Zacharias M. Molecular Dynamics and Advanced Sampling Simulations of Nucleic Acids[J]. In: Leszczynski J. (eds) Handbook of Computational Chemistry. Springer, Dordrecht. Handbook of Computational Chemistry, 2015.
* For Research Use Only.