BALLView Documentation: Molecular Mechanics

## Index ## Molecular Mechanics BALLView provides a wide variety of Molecular Mechanics features: Single point energies Minimizations Molecular dynamics simulations ## Using selections For 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 fields When 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: Missing atoms, e.g. hydrogens Invalid bonds, e.g. covalent bonds instead of ion bonds Force field is not suited for target molecule (MMFF94 can e.g. not handle nucleic acids) Possible solutions: Adding missing atoms (see "Build" menu) Deleting unsupported compounds/ligands through the MolecularControl Manually fixing errors through the editing mode Choosing an other force field ## Single point energies BALLView 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. ## Minimizations Currently BALLView support four different minimizers: Shifted LVMM L-BFGS Conjugate Gradient Steepest Descent These minimizers can be combined with any of the integrated force fields. Moreover, users can freely choose the stop conditions, like the maximum number of iterations, energy difference or gradient. If any of these conditions is met, the minimization ends. Since the minimization is implemented with multithreading techniques users can freely reposition the camera and thus e.g. focus on a given functional group. ## Molecular dynamics simulations BALLView 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. ## Index