LINK to article
J Chem Theory Comput. 2016 Nov 8;12(11):5541-5548. Epub 2016 Oct 24.
Reverse Coarse-Graining for Equation-Free Modeling: Application to Multiscale Molecular Dynamics.
Abi Mansour A1, Ortoleva PJ1.
- Department of Chemistry and Center for Theoretical and Computational Nanoscience, Indiana University , Bloomington, Indiana 47405, United States.
Constructing atom-resolved states from low-resolution data is of practical importance in many areas of science and engineering. This problem is addressed in this article in the context of multiscale factorization methods for molecular dynamics. These methods capture the crosstalk between atomic and coarse-grained scales arising in macromolecular systems. This crosstalk is accounted for by Trotter factorization, which is used to separate the all-atom from the coarse-grained phases of the computation. In this approach, short molecular dynamics runs are used to advance in time the coarse-grained variables, which in turn guide the all-atom state. To achieve this coevolution, an all-atom microstate consistent with the updated coarse-grained variables must be recovered. This recovery is cast here as a nonlinear optimization problem that is solved with a quasi-Newton method. The approach yields a Boltzmann-relevant microstate whose coarse-grained representation and some of its fine-scale features are preserved. Embedding this algorithm in multiscale factorization is shown to be accurate and scalable for simulating proteins and their assemblies.