Solvent Reorganization Energies in A-DNA, B-DNA, and Rhodamine 6G−DNA Complexes from Molecular Dynamics Simulations with a Polarizable Force Field

2009 ◽  
Vol 113 (13) ◽  
pp. 4425-4434 ◽  
Author(s):  
Egor Vladimirov ◽  
Anela Ivanova ◽  
Notker Rösch
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Rhodamine 6G ◽  
Dna Complexes ◽  
Polarizable Force Field ◽  
Reorganization Energies ◽  
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.

Structure of Rhodamine 6G−DNA Complexes from Molecular Dynamics Simulations

2007 ◽  
Vol 8 (11) ◽  
pp. 3429-3438 ◽  
Author(s):  
Anela Ivanova ◽  
Grzegorz Jezierski ◽  
Egor Vladimirov ◽  
Notker Rösch
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Rhodamine 6G ◽  
Dna Complexes ◽  
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
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