title: Introduction of steered molecular dynamics into UNRES coarse-grained simulations package.
abstract: In this article, an implementation of steered molecular dynamics (SMD) in coarse-grain UNited RESidue (UNRES) simulations package is presented. Two variants of SMD have been implemented: with a constant force and a constant velocity. The huge advantage of SMD implementation in the UNRES force field is that it allows to pull with the speed significantly lower than the accessible pulling speed in simulations with all-atom representation of a system, with respect to a reasonable computational time. Therefore, obtaining pulling speed closer to those which appear in the atomic force spectroscopy is possible. The newly implemented method has been tested for behavior in a microcanonical run to verify the influence of introduction of artificial constrains on keeping total energy of the system. Moreover, as time dependent artificial force was introduced, the thermostat behavior was tested. The new method was also tested via unfolding of the Fn3 domain of human contactin 1 protein and the I27 titin domain. Obtained results were compared with Gø-like force field, all-atom force field, and experimental results. © 2017 Wiley Periodicals, Inc.
authors.affiliation: Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk, 80-308, Poland.
authors.forename: Adam K
authors.initials: AK
authors.lastname: Sieradzan
authors.affiliation: Faculty of Physics, Astronomy and Informatics, Institute of Physics, Nicolaus Copernicus University, Grudziadzka 5, Torun, 87-100, Poland.
authors.forename: Rafał
authors.initials: R
authors.lastname: Jakubowski
keywords: atomic force microscopy; coarse-grain force field; protein mechanical stability