Abstract
The application of classical molecular dynamics (MD) simulations at atomic resolution (fine-grained (FG) level), to the majority of biomolecular processes, remains limited because of the associated computational complexity of representing all the atoms. This problem is magnified in presence of protein-based biomolecular systems that have a very large conformational space and MD simulations with FG resolution have slow dynamics to explore this space. Current transferrable coarse-grained (CG) force fields in literature are either limited to only peptides with the environment encoded in an implicit form (cannot study environmental heterogeneity) or cannot capture transitions into secondary/tertiary peptide structures from a primary sequence of amino acids.
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