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Sunday28 February 2021

How to effectively run molecular dynamics simulations with AMBER?

amberToday we are going to review a case study of University of Illinois “Accelerated molecular modelling enables rapid response to H1N1” that shows how scientists could efficiently run multiple simulations and potentially achieve life-saving results faster.

In response to a global pandemic, like Influenza A, requires a quick development of drugs to effectively treat a new virus that is likely to evolve. A research group of University of Illinois, Urbana- Champaign, was using Amber Molecular Dynamics, a suite of computational chemistry programs and force fields for molecular dynamics, on its study of Influenza A (H1N1) virus. The main challenge for the scientists was the duration of each simulation cycle per day as more simulations meant faster time to discovery.

Development of drugs comprises several processes, one of which is a compute-intensive process that is used to define how mutations of the flu virus protein could disrupt the binding pathway of the vaccine Tamiflu, rendering of this process could be potentially ineffective. This determination involved a daunting simulation of a 35,000- atom system, something that Urbana- Champaign scientists decided to tackle in a new way using NVIDIA GPUs. Managing these simulations on a CPU could take more than a month to calculate, and that would only amount to a single simulation, not the multiple simulations that constitute a complete study.

Using Amber and Tesla GPUs accelerators to perform molecular modelling calculations and simulate the drug resistance of H1N1 mutations, allowed the research group University of Illinois to complete the simulation in just over an hour.  The almost thousand fold improvement in performance available through GPU computing and advanced algorithms empowered the scientists to perform “emergency computing” to examine biological problems of extreme relevance and share their results with the medical research community. The increase in speed allowed researchers to achieve their original goal, testing Tamiflu’s efficacy in treating H1N1 and its mutations, and gave them time to make other important discoveries.

The use of GPUs in the research has enabled scientist to produce actionable results about the efficacy of Tamiflu during a single afternoon, while conventional approaches would take weeks or months to show the same results.

Our Technical team has done its own experiment and stated that a single NVIDIA GPU accelerates Amber a performance and gives the results that are comparable to HPC cluster with 4 nodes for simple simulations (JAC benchmark):


Up to 16 nodes for more complicated simulations such as 25095 Atom Nucleosome:


You can accelerate your research up to x25 times by using GPU while running Amber 12 application.
Test more theories, simulate different scenarios and do more science every single day with advanced technologies!

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