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Introduction of periodic boundary conditions into UNRES force field
Author(s) -
Sieradzan Adam K.
Publication year - 2015
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.23864
Subject(s) - force field (fiction) , boundary (topology) , periodic boundary conditions , field (mathematics) , physics , mechanics , classical mechanics , chemistry , boundary value problem , mathematics , mathematical analysis , pure mathematics , quantum mechanics
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. © 2015 Wiley Periodicals, Inc.