Variational Scheme to Compute Protein Reaction Pathways using Atomistic Force Fields with Explicit Solvent
Autor: | Beccara, S. a, Fant, L., Faccioli, P. |
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Rok vydání: | 2014 |
Předmět: | |
Druh dokumentu: | Working Paper |
Popis: | 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. Comment: Accepted for publication on Phys. Rev. Lett |
Databáze: | arXiv |
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