Variational Scheme to Compute Protein Reaction Pathways using Atomistic Force Fields with Explicit Solvent

S. a Beccara; L. Fant; P. Faccioli

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arXiv · 1405.6104

Variational Scheme to Compute Protein Reaction Pathways using Atomistic Force Fields with Explicit Solvent

S. a Beccara·L. Fant·P. Faccioli

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Abstract

We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding, using state of the art all-atom force fields in explicit solvent. We test this method against molecular dynamics (MD) simulations of the folding of an alpha- and a beta-protein performed with the same all-atom force field on the Anton supercomputer. We find that our approach yields results consistent with those of MD simulations, at a computational cost orders of magnitude smaller.

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S. a Beccara, L. Fant, P. Faccioli. 2015-02-18. Variational Scheme to Compute Protein Reaction Pathways using Atomistic Force Fields with Explicit Solvent. https://arxiv.org/abs/1405.6104

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