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Abstract

The Accelerated Weight Histogram method (AWH) is an enhanced sampling technique for molecular dynamics simulations, capable of speeding up expensive computational tasks such as sampling protein conformational changes or computing binding free energies.

Here, we present two new tutorials on how to use AWH within the molecular dynamics engine, GROMACS. In the first tutorial, awh-basic, we will learn the theory behind AWH and how to use it to study the interactions of two small molecules in solution by deriving the potential of mean force. At the end of the tutorial, we will also compare the results to those obtained from another enhanced sampling technique, umbrella sampling. In the second tutorial, awh-advanced, we will expand the theoretical discussion and add multi-dimensional reaction coordinates, modified target distributions, complex pulling coordinates, and finally introduce computational parallelization in the form of multiple walkers. This tutorial will result in complex free energy landscapes describing the conformational space of a small protein.

We hope that these tutorials will demonstrate ways to use AWH to solve real scientific problems, for the novice and advanced user alike.

Presenters

Claudia Alleva earned her Ph.D. in Biophysics in Forschungszentrum Jülich in 2019 and since then has focused on membrane transporters, aiming to characterize conformational changes responsible for the coupling of cotransported species (i.e. sodium and protons).

LinkedIn: @claudia-alleva

 

 

Cathrine Bergh earned her Ph.D. in theoretical biophysics in 2023 and now works as a researcher at the PDC Center for High-Performance Computing in Stockholm, Sweden. Her work has mostly focused on developing computational techniques to understand large conformational changes of proteins and protein-ligand interactions, e.g. through Markov state models, elastic network simulations, or large-scale HPC+AI workflows.

LinkedIn: @cathrine-bergh