Enhanced Sampling in Molecular Dynamics Simulations with Julia | Pablo Zubieta | JuliaCon 2021

This talk was presented as part of JuliaCon 2021.

Abstract:
When performing molecular dynamics simulations of materials in chemistry, physics and biology, there exists a large gap between the time scales that can be probed computationally to the ones observed in experiments. Two strategies to tackle this problem are both to develop algorithms to explore the simulation space more efficiently, and to employ hardware accelerators. I would like to share my experience and perspectives using Julia to make faster developments in both fronts.

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Contents
0:00 Welcome!
0:20 Two the most common approaches to molecular dynamics
0:37 What is enhanced sampling in molecular dynamics?
1:25 Various flavors of enhanced sampling
1:42 State of software suitable for advanced general ensemble simulations
2:10 Enhanced Sampling on GPUs
2:38 Our goal: improve the performance of the existing solutions
3:45 Overview of my workflow
5:16 What Julia brings to my work with C++ and Python?
5:40 Julia libraries that I wrote as a byproduct: DLPack.jl, ReactionCoordinates.jl, SSAGES.jl
5:55 Performance comparison
6:41 Example: alanine dipeptide in water
7:41 Conclusions

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