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.
@article{arxiv.1405.6104,
title = {Variational Scheme to Compute Protein Reaction Pathways using Atomistic Force Fields with Explicit Solvent},
author = {S. a Beccara and L. Fant and P. Faccioli},
journal= {arXiv preprint arXiv:1405.6104},
year = {2015}
}