Introduction of PBC
The larger number of atoms in a realistic system, restrict the system size of molecular simulation. For example, 12 grams of graphite will contain about 6.023 x 10^23 carbon atoms. The current computational systems are nowhere near simulating such a large number of atoms.
One of the ingenious ways to carry out such a simulation is to use Periodic Boundary Conditions(PBC). Using PBC, we approximate an infinite system using a smaller unit cell. For example, the graphite lattice can be seen as a repetition of the atoms unit cell shown.
When one of the atoms leave the unit cell from the surface, it renters the unit cell from the opposite surface.
Problem with PBC
One of the problems is using PBC is molecules being split over the periodic boundary. This leads to error in the calculation of properties like the center of mass or center of geometry. The goal of this project is to solve this problem.
The plan is to unwrap the molecules before performing the calculations. A significant part of the project is implementing unwrapping for structures which are not entirely bonded like DNA. The current plan of action is to create a reference point around which the structure will be unwrapped. After the implementation of unwrapping, the keyword ‘unwrap’ will be added to different methods, where it is needed.
1) An essential part of the project is to create a comprehensive testing environment for ‘unwrap’ method. 2) Adding benchmarks for the methods