title: Introduction of periodic boundary conditions into UNRES force field.
abstract: In this article, implementation of periodic boundary conditions (PBC) into physics-based coarse-grained UNited RESidue (UNRES) force field is presented, which replaces droplet-like restraints previously used. Droplet-like restraints are necessary to keep multichain systems together and prevent them from dissolving to infinitely low concentration. As an alternative for droplet-like restrains cuboid PBCs with imaging of the molecules were introduced. Owing to this modification, artificial forces which arose from restraints keeping a droplet together were eliminated what leads to more realistic trajectories. Due to computational reasons cutoff and smoothing functions were introduced on the long range interactions. The UNRES force field with PBC was tested by performing microcanonical simulations. Moreover, to asses the behavior of the thermostat in PBCs Langevin and Berendsen thermostats were studied. The influence of PBCs on association pattern was compared with droplet-like restraints on the ββα hetero tetramer 1 protein system.
authors.affiliation: Department of Physics and Astronomy, Uppsala University, Ångströmlaboratoriet, Lägerhyddsvägen, 1,751 20 Uppsala, Sweden; Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland.
authors.forename: Adam K
authors.initials: AK
authors.lastname: Sieradzan
mesh_terms: D003198:Computer Simulation; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
chemical_list: D010455:Peptides; D011506:Proteins
keywords: coarse-grain force field; electrostatic interaction cutoff; multi-chain systems; periodicity; proteins