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Abstract

Molecular dynamics (MD) simulations are limited by their accessible time scales, and their predictive power varies greatly with the particular problem.  To overcome this limitation, MD simulations can be accelerated by means of enhanced-sampling schemes, many of which use collective variables to quantify the progress toward hard-to-reach states.  The “Colvars” (1) library is a widely used software package that implements a broad variety of collective variable-based schemes.  Beginning with the GROMACS 2024 release series, Colvars is now included in the standard GROMACS distribution, greatly simplifying its use in a simulation.  This webinar will briefly introduce the features of Colvars, and discuss them alongside other GROMACS features that are complemented or enhanced by Colvars. We will also present an interactive workflow for exploring collective variable space and preparing Colvars/GROMACS simulations using a VMD extension, the Colvars Dashboard.

(1) https://colvars.github.io/

Presenters

Giacomo Fiorin received a M.S. in physics from the University of Padua and a Ph.D. in biophysics from the International School for Advanced Studies in Trieste. He later moved to the USA, where he has been a postdoctoral researcher with Michael Klein and later a research-track faculty member of Temple University. In 2020 Giacomo became a staff scientist at the National Institutes of Health (NIH), associated with the labs of Lucy Forrest and José Faraldo-Gómez. Giacomo’s research uses atomically detailed simulations to understand how lipids and proteins govern the mechanics and morphology of a cell’s membrane. In parallel, Giacomo also manages computational resources for the Forrest and Faraldo-Gómez labs, and routinely advises his colleagues at NIH on leveraging high-performance computing in their research. Since 2007 Giacomo has developed, together with Jérôme Hénin and several other collaborators, the widely used collective variables (Colvars) software library for enhanced sampling simulations.

 

Hubert Santuz is a software engineer at the Laboratoire de Biochimie Théorique (LBT) of the Institut de Biologie Physico-Chimique (IBPC) in Paris with a background in computer science and structural bioinformatics. His main activities are the development of scientific software in collaboration with researchers, focusing on new methods for the visualization of biological molecules. He is the maintainer of the UnityMol software and also runs a visualization platform at the institute. He is also interested in molecular dynamics simulations. In particular, he wrote the GROMACS-Colvars interface.

 

 

Jérôme Hénin is a CNRS Research Director at the Laboratoire de Biochimie Théorique (LBT) of the Institut de Biologie Physico-Chimique (IBPC) in Paris. He was trained in Physical Chemistry and Computational Chemistry in France, then did postdoctoral work at University of Pennsylvania with Michael L Klein. He has been working as a CNRS researcher since 2009, in Marseille then Paris.

Jérôme’s research activity is divided between two areas: methodological and software development for molecular simulations, and the application of these methods to the study of biological membranes. On the methodological side, his objective is to find robust and efficient sampling methods for biomolecular problems, to produce solid software implementations of these methods, and to disseminate them widely within the community for maximum impact. To that effect, he co-founded, and jointly develops, together with Giacomo Fiorin, the Colvars software library for sampling using collective variables in molecular simulations.