Webinar: Molecular simulation control and extension with gmxapi for GROMACS. (2018-09-19) 1


BioExcel’s webinar series continue with a presentation by Eric Irrgang, Kasson Lab

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Abstract

gmxapi is a framework and front-end designed to support new methods in molecular simulation. A Python package provides a scriptable interface to manage ensembles of simulations. A C++ extension interface allows researchers to attach custom code to a high-performance GROMACS simulation. The first beta release (gmxapi 0.0.4 March, 2018) demonstrated a restrained ensemble simulation method implemented as a GROMACS plug-in and controlled with just a few lines of Python. (DOI: 10.1093/bioinformatics/bty484) Closer integration with GROMACS (through infrastructure developments currently under code review) will ensure software sustainability and performance.

Presenter

Eric Irrgang, Kasson Lab

M. Eric Irrgang
Eric completed his undergraduate degree at the University of Texas, Austin and his PhD in Materials Science & Engineering with Sharon Glotzer at the University of Michigan before joining the Kasson Lab as a postdoctoral fellow. Now he is building interfaces for flexible and extensible molecular dynamics simulation. Eric believes strongly in proper software engineering design and flexible simulation interfaces but keeps a soft spot in his heart for Monte Carlo methods. He is supported by a MolSSI Software Fellowship.

Additional information:
gmxapi is a project in the Kasson Lab supported by NIH R01 GM115790, by a MolSSI fellowship (NSF ACI-1547580). In collaboration with other GROMACS developers at KTH,
University of Colorado, and globally.

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Title: Molecular simulation control and extension with gmxapi for GROMACS.

Date: 19th September, 2018
Time: 14:00 BST / 15:00 CEST

Registration URL: https://attendee.gotowebinar.com/register/8515339718336943875

Webinar ID: 532-343-491

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