Classical Molecular Dynamics

Work Package: 1

WP leader: Christoph Dellago, University of Vienna

Lead beneficiary: Technical University of Vienna

Classical simulations are increasingly applied in fields ranging from nanoscience and materials development to biomolecular engineering and drug design. This is facilitated by the existence of broad, consolidated software packages (e.g., LAMMPS, DL_POLY, Charmm, NAMD, GROMACS, OPENMM, AMBER) obviating the need to constantly develop new programmes and thus drastically reducing the effort to solve a particular problem. However, many processes of academic and industrial interest, such as protein folding, structural transitions of solid materials or study of phase behaviour for tailored material design, are still beyond standard simulation tools. In fact, disparate time scales (femtoseconds to milliseconds or even longer), originating from rare barrier crossing events, characterise these processes and require the accurate reproduction of the dynamics both on short and long time scales, imposing excessively long simulation times. In the last few years, modelling of rare events has made tremendous progress and several computational methods have been put forward to bridge the time scale gap. However, these new approaches have not been included yet, with adequate efficiency and scalability, in common simulation packages, mostly because their application requires some specialised expert knowledge, WP 1 will fill this gap.

WP 1 will provide a means for academics and industrialists to address computational questions that involve classical MD calculations reliably and effectively by implementing a set of coordinated actions aimed at industrial discussion, software development, and training. Topics such as trajectory sampling algorithms and statistical tools to identify reaction coordinates will be addressed in the early stages of the project.

To facilitate industrial discussion, the classical MD team will organise 2 industry workshops and complete one pilot project with Biki Technologies.

For software development and training, 5 extended software development workshops will be organised and the classical MD part of the E-CAM software repository will be developed. This will be based around software modules for rare events modelling. Continuous monitoring of requests from the end users and reassessment of the state-of-the-art in the field will guide software developments and industrial discussion.

The state-of-the art will be reviewed through the organisation of 2 state-of-the-art workshops during the funding period.

Tag: Classical MD