Research Highlights

Reproducible MD Simulation on Amber GPU



With the click of a button, a simulation is triggered and a user can visualize the dance a protein performs in a solution.

Described above is the combined power of Kepler and Molecular Dynamic (MD) simulations. MD simulation is a powerful tool to study the atomistic details of a biological system. Atom movements across time are predicted by solving Newton’s equation. The result is a movie depicting a protein dance performed by underlying atoms. However, MD simulation has several downfalls, especially when it comes to reproducibility. It is cumbersome to record every simulation run and pass it on to another researcher. The simulation itself is also difficult to set up for inexperienced users. To combat these issues, NBCR scientists found another more reliable source — Kepler — to make MD simulations more accessible or reproducible.  

Kepler workflows have been a big part of NBCR in recent years. Kepler is an open source platform for building scientific workflows. Similar to making a movie, a Kepler workflow has a “director” and many “actors” to perform certain acts. To simplify further, a Kepler workflow is made of multiple components, and like a movie, the acts (components) are strung together to tell a story. Many of NBCR research procedures, including the protocols used to run MD simulations, are documented and recreated using workflows so they are available and can be evaluated by the scientific community. 

One of our latest and more compelling workflows is the Kepler Amber GPU workflow [1]. This workflow documents the steps needed to run an MD simulation and automates the MD process. So, you can sit back and relax knowing that the workflow will keep the simulation running and will deliver the data when the process is complete. 

You can download the workflow here (LINK)

Check out the workflow tutorial on BBDTC (LINK)



[1]. Purawat, S., P. U. Ieong, R. D. Malmstrom, G. J. Chan, A. K. Yeung, R. C. Walker, I. Altintas, and R. E. Amaro. 2017. A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics. Biophysical Journal 112:2469-2474.