Biomolecular Simulations of Halogen Bonds with a GROMOS Force Field

2018 ◽  
Vol 14 (10) ◽  
pp. 5383-5392 ◽  
Author(s):  
Rafael Nunes ◽  
Diogo Vila-Viçosa ◽  
Miguel Machuqueiro ◽  
Paulo J. Costa
Keyword(s):  
Force Field ◽  
Halogen Bonds ◽  
Biomolecular Simulations ◽  
Gromos Force Field

scholarly journals Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations

2012 ◽  
Vol 33 (31) ◽  
pp. 2451-2468 ◽  
Author(s):  
Wenbo Yu ◽  
Xibing He ◽  
Kenno Vanommeslaeghe ◽  
Alexander D. MacKerell
Keyword(s):  
Force Field ◽  
Biomolecular Simulations ◽  
General Force

scholarly journals Kinetic pathways of water exchange in the first hydration shell of magnesium: Influence of water model and ionic force field

2021 ◽  
Author(s):  
Sebastian Falkner ◽  
Nadine Schwierz
Keyword(s):  
Force Field ◽  
Water Exchange ◽  
Force Fields ◽  
Hydration Shell ◽  
Water Model ◽  
Polarizable Force Fields ◽  
Ionic Force ◽  
Influence Of Water ◽  
Biomolecular Simulations ◽  
Dynamics Simulations

Water exchange between the first and second hydration shell is essential for the role of Mg2+ in biochemical processes. In order to provide microscopic insights into the exchange mechanism, we resolve the exchange pathways by all-atom molecular dynamics simulations and transition path sampling. Since the exchange kinetics relies on the choice of the water model and the ionic force field, we systematically investigate the influence of seven different polarizable and non-polarizable water and three different Mg2+ models. In all cases, water exchange can occur either via an indirect or direct mechanism (exchanging molecules occupy different/same position on water octahedron). In addition, the results reveal a crossover from an interchange dissociative (Id) to an associative (Ia) reaction mechanism dependent on the range of the Mg2+-water interaction potential of the respective force field. Standard non-polarizable force fields follow the Id mechanism in agreement with experimental results. By contrast, polarizable and long-ranged non-polarizable force fields follow the Ia mechanism. Our results provide a comprehensive view on the influence of the water model and ionic force field on the exchange dynamics and the foundation to assess the choice of the force field in biomolecular simulations.

scholarly journals Definition and testing of the GROMOS force-field versions 54A7 and 54B7

2011 ◽  
Vol 40 (7) ◽  
pp. 843-856 ◽  
Author(s):  
Nathan Schmid ◽  
Andreas P. Eichenberger ◽  
Alexandra Choutko ◽  
Sereina Riniker ◽  
Moritz Winger ◽  
...  
Keyword(s):  
Force Field ◽  
Gromos Force Field

scholarly journals Force Field Model of Periodic Trends in Biomolecular Halogen Bonds

2014 ◽  
Vol 119 (29) ◽  
pp. 9140-9149 ◽  
Author(s):  
Matthew R. Scholfield ◽  
Melissa Coates Ford ◽  
Crystal M. Vander Zanden ◽  
M. Marie Billman ◽  
P. Shing Ho ◽  
...  
Keyword(s):  
Force Field ◽  
Field Model ◽  
Halogen Bonds

Spontaneous Formation of KCl Aggregates in Biomolecular Simulations: A Force Field Issue?

2007 ◽  
Vol 3 (5) ◽  
pp. 1851-1859 ◽  
Author(s):  
Pascal Auffinger ◽  
Thomas E. Cheatham ◽  
Andrea C. Vaiana
Keyword(s):  
Force Field ◽  
Spontaneous Formation ◽  
Biomolecular Simulations
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