Andrzej Kolinski Research Group

Coarse-grained protein modeling

Modeling Software & Servers

Biomolecules — dynamics & interactions


Toward more efficient simulations of slow processes in large biomolecular systems: Comment on "Ligand diffusion in proteins via enhanced sampling in molecular dynamics" by Jakub Rydzewski and Wieslaw Nowak.


Physics of Life Reviews, 22–23:85-87, 2017


Molecular Dynamics is a powerful computational method for studying the structure, energetics and dynamics of molecular objects. Since the available computing power grows rapidly, satisfying over the last 50 years the famous Moore's Law, larger and more complex systems can be effectively modeled using the MD tools. Nevertheless, many problems of molecular biology or biophysics are still beyond the reach of efficient applicability with classical MD. Simply, interesting biomolecular systems are often huge, composed of thousands (many thousands) of atoms, and the characteristic time scale of important processes can range from seconds to several days. Modeling of ligand diffusion, discussed in the review by Rydzewski and Nowak, is one of such complex MD tasks located on the border of the applicability of classical MD algorithms. The problems discussed in the review are important not only for molecular physics and chemistry, but they could also be very interesting for rational drug design, especially since experimental ligand diffusion data are difficult to collect and interpret.