scholarly journals Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks

2018 ◽  
Vol 39 (21) ◽  
pp. 1682-1689 ◽  
Author(s):  
Jing Huang ◽  
Justin A. Lemkul ◽  
Peter K. Eastman ◽  
Alexander D. MacKerell
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Polarizable Force Field ◽  
Dynamics Simulations

scholarly journals Vibrational mode assignment of finite temperature infrared spectra using the AMOEBA polarizable force field

2015 ◽  
Vol 17 (39) ◽  
pp. 25968-25977 ◽  
Author(s):  
Florian Thaunay ◽  
Jean-Pierre Dognon ◽  
Gilles Ohanessian ◽  
Carine Clavaguéra
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Infrared Spectra ◽  
Finite Temperature ◽  
Vibrational Mode ◽  
Vibrational Modes ◽  
Polarizable Force Field ◽  
Dynamics Simulations ◽  
Mode Assignment

The Driven Molecular Dynamics approach has been adapted and associated with the AMOEBA polarizable force field to assign and visualize vibrational modes in infrared spectra obtained by molecular dynamics simulations.

scholarly journals A Polarizable Force Field of Dipalmitoylphosphatidylcholine Based on the Classical Drude Model for Molecular Dynamics Simulations of Lipids

2013 ◽  
Vol 117 (31) ◽  
pp. 9142-9160 ◽  
Author(s):  
Janamejaya Chowdhary ◽  
Edward Harder ◽  
Pedro E. M. Lopes ◽  
Lei Huang ◽  
Alexander D. MacKerell ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Drude Model ◽  
Polarizable Force Field ◽  
Dynamics Simulations

scholarly journals Drude Polarizable Force Field for Molecular Dynamics Simulations of Saturated and Unsaturated Zwitterionic Lipids

2017 ◽  
Vol 13 (9) ◽  
pp. 4535-4552 ◽  
Author(s):  
Hui Li ◽  
Janamejaya Chowdhary ◽  
Lei Huang ◽  
Xibing He ◽  
Alexander D. MacKerell ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Polarizable Force Field ◽  
Zwitterionic Lipids ◽  
Dynamics Simulations
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