dnaMolecular Dynamics simulation is one the most rapidly growing methods for modelling in general, and for life science in particular. As an example, since 2009 more papers have been published annually using molecular dynamics simulations than have presented nuclear magnetic resonance studies of proteins.

MD simulations are one of the largest consumers of supercomputing resources, and advances in hardware as well as software (e.g. packages like GROMACS, NAMD, Amber, LAMMPS, Desmond) have enabled simulations of macromolecules with hundreds of thousands of atoms. While this provides time resolution most experimental methods cannot provide, the available simulation lengths are still orders of magnitude below important biological processes.

GROMACS is a major open source and free software package for biomolecular simulation and is developed as an international collaboration steered from KTH, Sweden. The traditional strong point of GROMACS has been exceptionally high efficiency, which is also the reason it is used as the engine in Folding@Home.

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