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Hamiltonian replica‐exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles
Authors:Katja Ostermeir  Martin Zacharias
Institution:Physik‐Department T38, Technische Universit?t München, Garching, Germany
Abstract:A Hamiltonian Replica‐Exchange Molecular Dynamics (REMD) simulation method has been developed that employs a two‐dimensional backbone and one‐dimensional side chain biasing potential specifically to promote conformational transitions in peptides. To exploit the replica framework optimally, the level of the biasing potential in each replica was appropriately adapted during the simulations. This resulted in both high exchange rates between neighboring replicas and improved occupancy/flow of all conformers in each replica. The performance of the approach was tested on several peptide and protein systems and compared with regular MD simulations and previous REMD studies. Improved sampling of relevant conformational states was observed for unrestrained protein and peptide folding simulations as well as for refinement of a loop structure with restricted mobility of loop flanking protein regions. © 2013 Wiley Periodicals, Inc.
Keywords:molecular dynamics simulations  peptide and protein folding  potential scaling  conformational sampling  accelerated sampling  force field calculation
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