A method for modeling icosahedral virions: Rotational symmetry boundary conditions

We present two techniques for implementing a new method of simulating an entire virion. Earlier computer simulations of a capsid protein revealed large edge effects due to the use of free standing boundaries. Because of the size of a given protomer, conventional three‐dimensional periodic boundary conditions would be extremely wasteful. This would require an extremely large number of solvent molecules, and therefore would be computationally feasible for only a fragment of the entire virion. The new method employs non‐space‐filling computational cells in molecular modeling and molecular dynamics with the boundary conditions based on the icosahedral group. The method is general and could be used for any molecular system with a point group symmetry. With this method, the dynamical and spatial intra and interprotomer correlations can be studied at atomic levels. The technique is applicable to any virion with icosahedral symmetry. A sample calculation involving a geometry optimization of the human rhinovirus coat proteins is given to demonstrate the technique.