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 Polarizable General Force Field for Drug-Like Molecules: Drude General Force Field (DGenFF)

2019 ◽  
Vol 116 (3) ◽  
pp. 142a ◽  
Author(s):  
Payal Chatterjee ◽  
Esther Heid ◽  
Christian Schröder ◽  
Alexander D. MacKerell
Keyword(s):  
Force Field ◽  
General Force

On the development of a general force field for the molecular simulation of perfluoroethers

2003 ◽  
Vol 101 (14) ◽  
pp. 2157-2169 ◽  
Author(s):  
H.-C. LI ◽  
C. MCCABE ◽  
S. T. CUI ◽  
P. T. CUMMINGS ◽  
H. D. COCHRAN
Keyword(s):  
Force Field ◽  
Molecular Simulation ◽  
General Force

scholarly journals Automation of the Charmm General Force Field for Drug-Like Molecules

2011 ◽  
Vol 100 (3) ◽  
pp. 611a ◽  
Author(s):  
Kenno Vanommeslaeghe ◽  
Jayeeta Ghosh ◽  
Narendra K. Polani ◽  
Michael Sheetz ◽  
Sudhakar V. Pamidighantam ◽  
...  
Keyword(s):  
Force Field ◽  
General Force

scholarly journals Completeness of the Trajectories of Particles Coupled to a General Force Field

2012 ◽  
Vol 208 (1) ◽  
pp. 255-274 ◽  
Author(s):  
Anna Maria Candela ◽  
Alfonso Romero ◽  
Miguel Sánchez
Keyword(s):  
Force Field ◽  
General Force

scholarly journals Development and Benchmarking of Open Force Field v1.0.0, the Parsley Small Molecule Force Field

2020 ◽  
Author(s):  
Yudong Qiu ◽  
Daniel Smith ◽  
Simon Boothroyd ◽  
Hyesu Jang ◽  
Jeffrey Wagner ◽  
...  
Keyword(s):  
Force Field ◽  
Small Molecule ◽  
Data Types ◽  
Software Ecosystem ◽  
Energy Profiles ◽  
Torsion Potential ◽  
Full Optimization ◽  
General Force ◽  
Chemical Perception ◽  
Natural Means

We describe the structure and optimization of the Open Force Field 1.0.0 small molecule force field, code-named Parsley. Parsley uses the SMIRKS-native Open Force Field (SMIRNOFF) parameter assignment formalism in which parameter types are assigned directly by chemical perception, in contrast to traditional atom type-based approaches. This method provides a natural means to incorporate increasingly diverse chemistry without needlessly increasing force field complexity. In this work, we present essentially a full optimization of the valence parameters in the force field. The optimization was carried out with the ForceBalance tool and was informed by reference quantum chemical data that include torsion potential energy profiles, optimized gas-phase structures, and vibrational frequencies. These data were computed and are maintained with QCArchive, an open-source and freely available distributed computing and database software ecosystem. Tests of the resulting force field against compounds and data types outside the training set show improvements in optimized geometries and conformational energetics and demonstrate that Parsley's accuracy for liquid properties is similar to that of other general force fields. <br>

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 Extension of the CHARMM General Force Field to Linked Nitrogen-Containing Hetreroaromatic Rings

2015 ◽  
Vol 108 (2) ◽  
pp. 160a ◽  
Author(s):  
Lei Fang ◽  
Ignacio Soteras Gutiérrez ◽  
Kenno Vanommeslaeghe ◽  
Alexander D. MacKerell
Keyword(s):  
Force Field ◽  
General Force
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