scholarly journals ORAC: A molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level

2009 ◽  
pp. NA-NA ◽  
Author(s):  
Simone Marsili ◽  
Giorgio Federico Signorini ◽  
Riccardo Chelli ◽  
Massimo Marchi ◽  
Piero Procacci
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Simulation Program ◽  
Biomolecular Systems ◽  
Energy Surfaces

Nonadiabatic molecular dynamics simulation for the ultrafast photoisomerization of dMe-OMe-NAIP based on TDDFT on-the-fly potential energy surfaces

2021 ◽  
Vol 23 (9) ◽  
pp. 5236-5243
Author(s):  
Ying Hu ◽  
Chao Xu ◽  
Linfeng Ye ◽  
Feng Long Gu ◽  
Chaoyuan Zhu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Potential Energy ◽  
Potential Energy Surfaces ◽  
Dynamics Simulation ◽  
Surface Hopping ◽  
Nonadiabatic Molecular Dynamics ◽  
Energy Surfaces

Global switching on-the-fly trajectory surface hopping molecular dynamics simulation was performed on the accurate TD-B3LYP/6-31G* potential energy surfaces for E-to-Z and Z-to-E photoisomerization of dMe-OMe-NAIP up to S1(ππ*) excitation.

scholarly journals Free Energy Profile of APOBEC3G Protein Calculated by a Molecular Dynamics Simulation

Biology ◽  
2012 ◽  
Vol 1 (2) ◽  
pp. 245-259
Author(s):  
Yoshifumi Fukunishi ◽  
Saki Hongo ◽  
Masami Lintuluoto ◽  
Hiroshi Matsuo
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Energy Profile ◽  
Free Energy Profile
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