Eighth shell method has previously been shown to be the most optimal in terms of parallelization over large number of nodes. However, this method supports only the P1 periodic boundary condition and cannot handle reflection and/or rotational symmetry. We have developed the Extended Eighth shell method – it simulates only the asymmetric unit and communicates coordinates and images with images that correspond to P21 PBC. Reciprocal space calculations are done after applying the symmetry operation to create the full unit cell. P21 PBC has application in lipid bilayer simulations as it allows the movement of lipids from one layer to the other, thus balancing the chemical potential difference between the two layers. In simulations of Au nanoparticles in a DPPC bilayer, we compare the PMF of insertion of the nanoparticles under P1 and P21 PBC and demonstrate the importance of balancing of chemical equilibrium.

Extended eighth-shell method for periodic boundary conditions with rotations

2019 Spring National Meeting

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