Molecular Dynamics in AMS

The Amsterdam Modeling Suite offers powerfull Molecular Dynamics (MD) and Monte Carlo (MC) functionality. With plenty of advanced MD functionality and trajectory analysis tools, as well as excellent parallel scalability, AMS has been a popular choice for MD simulations. Thanks to the AMS driver concept, MD settings can easily be ported between compute engines, both internal and external, e.g. via the interface to the atomic simulation environment (ASE) engine.

• Easy set up of complex systems via GUI: Solvation, Polymers, Crystal structures,…
• Various thermo- and barostats
• Accelerating MD: Long timescales, e.g. Collective Variable-driven Hyperdynamics (CVHD), Replica Exchange MD (REMD),…
• Metadynamics via PLUMED
• Polymer cross-linking via Bond Boost acceleration
• Molecule gun and molecule sink: depositing atoms and molecules, CVD, sputtering processes
• Non-equilibrium MD, e.g. thermal transport (T-NEMD)
• Trajectory analysis tools: Radial distribution functions, diffusion coefficients,…
• ChemTraYzer2: Fully automatic reaction network detection of species, reactions and rate constants
• Powerful scripting interface for automation of workflows
• High-perfomance hybrid parallelization (MPI, openMP)