MD course project


SNIC 2017/3-78


SNAC Small

Principal Investigator:

Michael Holmboe


UmeƄ universitet

Start Date:


End Date:


Primary Classification:

10506: Geokemi




Will host an international 2-day workshop on MD with Gromacs with 18 participants --------------------------------------- This 2-day workshop will offer fundamental theory and hands-on training in molecular dynamics (MD) simulations with a focus on biogeochemical systems, targeting beginners as well as experienced modelers who would like to use the Gromacs suite of MD simulation programs to study geochemical phenomena. Molecular dynamics simulations can be used to quantitatively predict many properties and reactions of relevance to mineralogy, biogeochemistry, and material properties of natural and engineered systems. Examples of recent work applying MD simulations include predictions of the structure, phase transitions, and dynamics of water; the molecular scale behaviour of fluids near mineral surfaces and in nanopores; the adsorption structure and selectivity of electrolyte ions and organic compounds at mineral-water interfaces; the aggregation of colloids and swelling properties of clay minerals; and the molecular scale basis of kinetic isotope effects. The lectures and tutorials of this workshop will cover the fundamentals of molecular mechanics and simulation ensembles, elementary molecular potential parameterization, and an introduction to widely used forcefields for liquid water, organic molecules, and minerals in geochemical systems, including CLAYFF (Cygan et al. 2004) and INTERFACE (Heinz et al. 2005, 2013). The workshop also will discuss different types of enhanced sampling and free energy methods, illustrated by examples from current research. The hands-on tutorials will describe methods for creating molecular systems (clays, zeolites, metal oxides and organic solutes) and input files, run simulations, and analyse simulation output to determine structural, dynamic, and thermodynamic properties. The hands-on part of the workshop will use the Gromacs MD simulation package, a free software distributed under the GNU General Public License.