Workshop: GROMACS in Riga

Benson Muite, University of Tartu

GROMACS is a free and open source parallel molecular dynamics software. It is used by a wide variety of people, particularly for biomolecular and chemistry simulations. It is one of the most efficient open source molecular dynamics packages with a strong community influenced development model and a wide userbase.

GROMACS can be run on multicore CPUs, GPUs and distributed memory parallel clusters. A two day GROMACS workshop was recently held in Riga, Latvia. The workshop introduced GROMACS and the GROMACS software development process to the participants. The broad range of participants made for lively discussion and community building.

The initial part of the workshop introduced the main principles behind molecular dynamics and then used Justin Lemkul’s tutorial material for an introduction to using GROMACS to simulate a protein (Lysozyme) in water. One of the main uses of molecular dynamics is to find minimum energy configurations of molecules. This is computationally expensive, so multiple ensemble simulations are typically done. Thus, the next part of the workshop introduced umbrella sampling and replica exchange molecular dynamics, which are heuristic techniques that can reduce the computation time needed to find physically interesting chemical/biological molecular configurations. The second day of the workshop introduced further areas where GROMACS is used. In some cases, classical molecular dynamics is insufficient to capture processes occuring in molecules such as enzymes. In such a case, one can couple molecular dynamics with the density functional based tight binding method. This enables rapid time to solution by only using computationally expensive quantum models where they are needed – this is particularly useful when simulating enzymes.

GROMACS can also be used to simulate ionic liquids. Understanding the properties of ionic liquids is of research interest due to their applications in battery design for electric vehicles. Another application area of molecular dynamics is in the simulation of materials that will separate gas mixtures. The last part of the workshop introduced more advanced sampling methods that are useful in drug design and understanding of stable protein configurations.

Workshop materials can be found here. Some related GROMACS video seminars can be found on the Bioexcel webinar youtube channel. The materials may be helpful to learn about computational chemistry and community developed high performance computing software.

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