Replica Exchange Molecular Dynamics (REMD) Services

Protein aggregation is associated with many human diseases, such as Alzheimer's disease (AD), Parkinson's disease (PD) and type 2 diabetes (T2D). Understanding the molecular mechanism of protein aggregation is essential for the development of therapy. Molecular dynamics (MD) simulation has proven to be a powerful tool for studying protein aggregation. However, it is difficult for conventional MD simulation to sample the entire conformation space of a complex protein system within an acceptable simulation time because it is easy to fall into a local minimum energy state. Many enhanced sampling methods have been developed. Among them, the replica exchange molecular dynamics (REMD) method has been particularly attractive. By combining MD simulation with Monte Carlo algorithm, the REMD method can easily overcome the high energy barrier and can fully sample the conformational space of proteins.

Process of REMD.Figure 1. Replica exchange molecular dynamics (REMD).

Our molecular dynamics simulation service but not limited to:

Features about our Replica Exchange Molecular Dynamics (REMD) service

  • CD ComputaBio can provide you with replica exchange molecular dynamics simulation.
  • In REMD, a series of non-interacting replica systems are rebuilt, covering a wide range of temperatures.
  • Separate molecular dynamics simulations can be performed for each copy. According to the Metropolis standard, the configuration of each copy adjacent in temperature can be exchanged.
  • REMD simulation can make the low-temperature configuration space escape from the lowest point of local potential energy.
  • Compared with traditional dynamics, REMD simulation can sample in a larger configuration space.

Our simulation services

Project name Replica Exchange Molecular Dynamics (REMD) services
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 Replica Exchange Molecular Dynamics (REMD) services

Step1 Define system.
Step2 According to the number of available processors and the temperature range to be sampled.
Step3 After obtaining the temperature distribution, equilibrate the system separately at N temperatures (use a separate .mdp file for each temperature).
Step4 Run a short-term REMD simulation to obtain an estimate of the exchange probability (about 100 ps can get a good estimate).
Step5 Choose an initial conformation at each temperature depending on the reason for running REMD.

Our advantages

  • We have cooperated with many universities or research institutions, and can provide consultation and suggestions for complex issues.
  • After all the calculations are completed, we can assist in writing English academic papers or patents, and provide submission suggestions.
  • Our researchers usually require a full understanding of biological experiments. They can quickly understand the project situation through a simple description, and quickly establish a feasible research plan according to the client's needs, saving a lot of time for literature research.

Replica Exchange Molecular Dynamics (REMD) services 2

CD ComputaBio offers a corresponding replica exchange molecular dynamics (REMD) services. Our molecular dynamics simulations provide accurate approximations of real molecular behaviors, and have proven to be very useful in understanding the biochemical basis of physiological events at different stages of drug development, even in different fields such as materials science. Our team of experts can provide up to one millisecond of simulation time for the system you choose, so you do not have to worry about technical issues. We can also analyze these results for you. 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.