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Halvan needs to be restarted due to a memory overflow
SNIC Cloud Computing Course at UPPMAX, May 16
Molecular Dynamics
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Classical Molecular Dynamics is a method based on statistical mechanics and the solution of Newton's equations of motion. Often all atoms are described as explicit particles (give or take a few) which interact via a classical potential surface. The atomic forces are determined from the negative gradient of the potential energy with respect to the particle positions. The equations of motion of the atoms are then found by integrating the atomic positions, velocities ... wrt time using finite difference methods.
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A large variety is found in the description of the potential surface, from simple pair-additive potential functions to sophisticated many-body, polarizable models and methods based on explicit solution of the electron structure (such as HF and DFT) with the atomic positions as parameters in each timestep. Several hybrid methods exist as well and are becoming increasingly popular.
Contact the Application Expert in Molecular Dynamics Daniel Spångberg.
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Efficient compression of trajectories
