In REMD, a series of non-interactive replica systems are reconstructed, covering a wide temperature range from low to high temperatures. Perform independent molecular dynamics simulations for each copy. According to the Metropolis standard, the configuration of each copy adjacent in temperature can be exchanged. Therefore, 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 a larger configuration space. But the disadvantage of this method is that the amount of calculation is very large, the number of copies is proportional to, and N is the degree of freedom of the system.
Figure 1. Illustration of replica exchange molecular dynamics (REMD) method.
Once the peptide and its surrounding environment are determined, it is necessary to determine the range of the temperature space to be sampled, the number of processors used, and the length of time for the simulation. The system, the number of copies, the range of temperature space and the temperature distribution determine the average exchange between copies Probability. These values should be the same for all replicas. For this reason, if it is assumed that there is no known bottleneck in the free energy space, the potential energy of the system is expected to increase with increasing temperature, so the temperature distribution of the replicas should obey the exponential distribution.
With the development of high-precision force fields and the development of powerful computers, molecular dynamics (MD) has become a universal tool for studying the complex structure, thermodynamics and dynamic processes of interdisciplinary real systems. Therefore, we can provide AI-based copy exchange dynamics simulation, repeat the iterative MD-AI-MD-AI process until the required sampling is obtained. These spaces encode all relevant slow dynamics in the system, while the remaining fast dynamics are effectively replaced. Then, each round of AI will put a given sample of the slow mode, and after that the information is used to initiate a new biased round. Switching along the slow mode will result in an increase in exploration, and any incremental increase in exploration can be used in another round of AI to more accurately estimate the slow mode. Then, the unbiased thermodynamic and kinetic information can be recovered from the AI-enhanced MD trajectory thus obtained using standard rated procedures.
|Replica Exchange Molecular Dynamics (REMD) Service
|Compared with standard molecular dynamics simulations, Replica Exchange Molecular Dynamics (REMD) is an enhanced sampling technique
|CD ComputaBio can provide umbrella sampling simulation of various systems
|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.
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