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Sunday, August 23, 2020

Software Suite Expedites Reproducible Computer Simulations

Broadly an excellent idea,  here for molecular simulation and design.   But in general its useful to have locally useful and validated libraries of simulations that can be selected for application. Especially if  'reproducible' is important.   And typically it should be if you care about risk.  It is rarer than you think to to have this in place.

Software Suite Expedites Reproducible Computer Simulations
Vanderbilt School of Engineering
July 8, 2020

Researchers at Vanderbilt University have developed a suite of open source software tools that expedites the process of reproducing computer simulations. It can be difficult to reproduce experiments and obtain the same results in some fields, mainly because details provided in peer-reviewed publications aren't sufficient to recreate the conditions of the original experiment. The Molecular Simulation and Design Framework (MoSDeF) aims to eliminate those by automating as many research steps as possible, with one component providing validated parameters and applying forcefields (mathematical models for how molecules interact with each other) automatically. All modules and workflows developed for MoSDeF build on the scientific Python stack, which simplifies the creation, atom-typing, and simulation of complex molecular models. Vanderbilt’s Clare McCabe said, “By using freely available tools designed for collaborative code development, such as GitHub and Slack, we are creating a community-developed effort.”  ... .'

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