OpenMM User Profile: Erik Lindahl, PhD

Erik Lindahl of Stockholm University uses OpenMM to speed up molecular simulations of membrane proteins and takes inspiration from Simbios’ professional approach to software development as he continues developing and maintaining GROMACS.

from http://biomedicalcomputationreview.org/content/simbios-bringing-biomedical-simulation-your-fingertips

 

Simbios provides two key benefits to Erik Lindahl, PhD, associate professor of computational structural biology at Stockholm University. First, he says, he values the speed provided by OpenMM. Lindahl’s research involves simulating membrane proteins and, he says, “having support for GPUs—that will be critical to speed up simulation throughput 10-fold.” He predicts that OpenMM will be widely used as a plug-in when it can do everything that people do in modern molecular simulation. “We are 95% there, but we still have a short way to go before the GPU is a drop-in replacement for the CPU.”

 

Second, says Lindahl, who develops and maintains GROMACS, a widely used molecular dynamics software package, “Simbios’ influence is making us take a more professional approach to software development.” Lindahl has watched as the Simbios team efficiently developed code with dozens of people involved while still keeping the code maintainable. “What I didn’t really appreciate before was the importance of having professional software developers,” he says. Simbios’ approach to developing modern software libraries on a large scale, getting them to interact with one another, documenting the code thoroughly, and getting everything working consistently—“That’s very different from a typical scientific project where the scientist develops the code they need for the next paper,” Lindahl says.

 

Simbios has also been pushing the field by releasing its tools under completely open licenses, Lindahl says. “So they are not just making things available ‘in theory and if you ask really hard,’ but they are putting it out there with thorough documentation and saying ‘Please use this.’”



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