Inferring molecular structure from Nuclear Magnetic Resonance (NMR) measurements requires an accurate forward model that can predict chemical shifts from 3D structure. Current forward models are limited to specific molecules...
Coarse grain (CG) molecular dynamics (MD) can simulate systems inaccessible to fine grain (FG) MD simulations. A CG simulation decreases the degrees of freedom by mapping atoms from an FG representation into agglomerate CG particles. The FG to CG mapping is not unique. Research into systematic selection of these mappings is challenging due to their combinatorial growth with respect to the number of atoms in a molecule. Here we present a method of reducing the total count of mappings by imposing molecular topology and symmetry constraints. The count reduction is illustrated by considering all mappings for nearly 49,889 molecules. The resulting number of mapping operators is still large, so we introduce hierarchical graphs which encode multiple CG mapping operators. The encoding method is demonstrated for methanol and a 14-mer peptide. This encoding provides a foundation to perform automated mapping selection.
The selection of coarse-grained (CG) mapping operators is a critical step for CG molecular dynamics (MD) simulation. It is still an open question about what is optimal for this choice...
This work investigates if preserving the symmetry of the underlying molecular graph of a given molecule when choosing a coarse-grained (CG) mapping significantly affects the CG model accuracy.
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