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Introduction of Periodic Boundary Conditions into UNRES Force Field
Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Theoretical Physics.
2015 (English)In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 36, no 12, 940-946 p.Article in journal (Refereed) Published
Abstract [en]

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 hetero tetramer 1 protein system.

Place, publisher, year, edition, pages
2015. Vol. 36, no 12, 940-946 p.
Keyword [en]
multi-chain systems, periodicity, coarse-grain force field, electrostatic interaction cutoff, proteins
National Category
Physical Sciences Chemical Sciences
URN: urn:nbn:se:uu:diva-252670DOI: 10.1002/jcc.23864ISI: 000352579100009PubMedID: 25753584OAI: oai:DiVA.org:uu-252670DiVA: diva2:814328
Available from: 2015-05-26 Created: 2015-05-11 Last updated: 2015-05-26Bibliographically approved

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Sieradzan, Adam K.
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