Umbrella Sampling Simulation Service

CD ComputaBio has extensive experience in the field of umbrella sampling services. Our researchers can quickly understand the situation of the project through simple descriptions, and quickly formulate feasible research plans according to the needs of customers, thus saving a lot of literature research time. We have independently or assisted clients to complete a large number of related topics, and many of our results have been published in various well-known journals.

Principle of umbrella sampling

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In the kinetic simulation of the quantum-classical hybrid method, the non-adiabatic catastrophe between the solute and the solvent is the key factor that determines the solute energy transition. Studies have shown that this kind of energy quantum transition in the vibrational non-adiabatic appearance often only occurs at the moment when a few systems have larger non-adiabatic parameters (statistically small probability events). Therefore, the traditional potential energy surface transition method (surface hopping) based on the non-adiabatic combination parameter not only has a large number of statistical sampling times, low efficiency, but also large statistical errors. In particular, for the restricted solution system, due to the non-uniformity of the solution structure, the above shortcomings will be particularly prominent in the process of investigating the energy relaxation of the solution system. In order to implement effective statistical sampling of the non-adiabatic coupling parameters, umbrella sampling is used, given the feasibility plan of investigating large non-adiabatic parameter sampling in the dynamic simulation of the quantum-classical hybrid method; derived the umbrella sampling potential system for the dynamic simulation of the quantum-classical hybrid method Hanitlton equation of motion and its numerical integration formula. This method can be used to investigate the molecular vibrational energy relaxation rate constant in the solution system.

Algorithm

The binding energy (ΔGbind) is derived from the potential of mean force (PMF), extracted from a series of umbrella sampling simulations. A series of initial configurations is generated, each corresponding to a location wherein the molecule of interest (generally referred to as a "ligand") is harmonically restrained at increasing center-of-mass (COM) distance from some other group via an umbrella biasing potential. This restraint allows the ligand to sample the configurational space in a defined region along a reaction coordinate defined between the two groups. The windows must allow for slight overlap of the ligand positions for proper reconstruction of the PMF curve.

Process of umbrella sampling simulation

Generate a series of configurations along a single degree of freedom (reaction coordinate).
Extract frames from the trajectory in step 1 that correspond to the desired COM spacing.
Run umbrella sampling simulations on each configuration to restrain it within a window corresponding to the chosen COM distance.
Use the Weighted Histogram Analysis Method (WHAM) to extract the PMF and calculate ΔG_bind.

Figure 1. Process of umbrella sampling simulation.

Service items

Project name	Umbrella sampling simulation service
Advantages	Few statistical sampling times required High sampling efficiency And the statistical error is small.
Services	CD ComputaBio can provide umbrella sampling simulation of various systems
Cycle	Depends on the time you need to simulate and the time required for the system to reach equilibrium.
Product delivery mode	The simulation results provide you with the raw data and analysis results of mbrella sampling simulation.
Price	Inquiry

Optional analysis items

For umbrella sampling simulation, the most common analysis is to obtain PMF and get the ΔG of the association/dissociation process
CD ComputaBio can analyze the statistical errors in umbrella sampling simulation through umbrella integration We can study the sources of different sampling errors, and derive the approximate expression analysis of statistical errors when using harmonic constraints and umbrella integration

Why choose us?

CD ComputaBio offers professional one-step umbrella sampling simulation service.
CD ComputaBio provides one-stop targeted services according to the detailed requirements of customers.
A wide range of systems that can be simulated and calculated.
A detailed report will be provided at the end of the whole project, including original data, result analysis, energy calculation, etc.
If you have any questions about our umbrella sampling simulation service, please contact us.

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