BALLView provides a wide variety of Molecular Mechanics features:
Using selectionsFor any of the above features, BALLView supports the application of arbitrary selections that can be used to restrict these calculations to a subset of atoms. This enables users, e.g., to optimize only the hydrogen atoms in a molecule: Such selections can either be created by applying a boolean expression or click on the checkbox for any item in the MolecularControl. But remember: These selections are only needed for restricting the calculations! In most of the times in suffices to highlight the molecular system (click on the name of the root item in the MolecularControl) and click on the corresponding entry in the "Molecular Mechanics" menu.
Problems with force fieldsWhen using the Molecular Mechanics features, users often experience problems with the the force field parametrization: If the atom typing process fails for some atoms or if no parameters can be found, BALLView selects these atoms for easier inspections. As a result, the atoms are marked in the MolecularControl and in the 3D graphics widget. If a given numbers of unassigned atoms is succeded, the calculation is aborted (see configuration dialog for the force field). The most common causes for unassigned atoms are:
Single point energiesBALLView support the calculation of energies with any of the integrated force fields. If a selection is applied to the molecule, the energy is only calculated for the selected atoms (see above). Along with the energy the forces and charges for the individual atoms are calculated.
MinimizationsCurrently BALLView support four different minimizers:
Molecular dynamics simulationsBALLView supports canonical and microcanonical MD simulations with any of the integrated force fields. Users can freely choose the number of steps, temperature and timestep. Here, it is important not to choose too large timesteps, since the simulations will become too inacurate and produce strange results. As a rule of thumb, the timestep should not get larger than 0.001 ps. While performing a MD simualtion, the resulting conformations can be stored as a trajectory in DCD format. This data can then be visualized as animation.