Sieradzan Adam K
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.
J Comput Chem. 2015 May 5;36(12):940-6. doi: 10.1002/jcc.23864. Epub 2015 Mar 8.
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.
本文介绍了将周期性边界条件（PBC）应用于基于物理的粗粒度联合残基（UNRES）力场，该方法取代了先前使用的液滴状约束。液滴状约束对于保持多链系统在一起并防止它们溶解到无限低浓度是必要的。作为液滴状约束的替代方法，引入了对分子进行成像的长方体PBC。由于这种修改，消除了由保持液滴在一起的约束产生的人工力，这导致了更真实的轨迹。出于计算原因，在长程相互作用上引入了截断和平滑函数。通过进行微正则模拟对具有PBC的UNRES力场进行了测试。此外，为了评估PBC中恒温器的行为，研究了朗之万恒温器和贝伦森恒温器。将PBC对缔合模式的影响与ββα异源四聚体1蛋白质系统上的液滴状约束进行了比较。
