. IntroductionVaccine computer-aide

. IntroductionVaccine computer-aided design (VCAD) computationally con-structs candidates for virus-like particles (VLPs), performsmolecular dynamics (MD) simulations to screen putative candi-dates, and therefore holds great promise for the efficient discoveryof vaccines.Key elements of the VCAD approach considered here includerevealing self-assembly pathways, assessing thermal stability, andpredicting likely immunogenicity for a target pathogen. However,VLP MD simulation places impractical demands on computationalresources, particularly in light of the many simulations needed inthe course of a VCAD project (e.g., to survey the effects of a range ofhost medium conditions, epitope sequences, and overall VLP struc-tures considered). Multiscale MD methods that (1) avoid the needfor calibrating [1] coarse-grained (CG) models (such as force match-ing [2], iterative Boltzmann inversion fitting [3], elastic networkmodels [4], etc), (2) provide atomic resolution based on interatomicforce fields, and (3) provide great efficiency over conventional MD,are now making this VLP VCAD possible.MD is a method to simulate the evolution in time