Redox Properties of Native and Damaged DNA from Mixed Quantum Mechanical/Molecular Mechanics Molecular Dynamics Simulations

2020 ◽  
Vol 16 (10) ◽  
pp. 6690-6701
Author(s):  
Polydefkis Diamantis ◽  
Ivano Tavernelli ◽  
Ursula Rothlisberger
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Mechanics ◽  
Redox Properties ◽  
Quantum Mechanical ◽  
Dynamics Simulations ◽  
Damaged Dna

scholarly journals QM/MM description of periodic systems

2015 ◽  
Vol 14 (07) ◽  
pp. 1550054 ◽  
Author(s):  
K. Doll ◽  
T. Jacob
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Mechanics ◽  
Liquid Water ◽  
Three Dimensional ◽  
Water Dimer ◽  
Periodic Systems ◽  
Quantum Mechanical ◽  
Dynamics Simulations

A quantum mechanical molecular mechanics (QM/MM) implementation for periodic systems is reported. This is done for the case of molecules and for systems with two and three-dimensional periodicity, which is suitable to model electrolytes in contact with electrodes. Tests on different water-containing systems, ranging from the water dimer up to liquid water indicate the correctness of the scheme. Furthermore, molecular dynamics simulations are performed, as a possible direction to study realistic systems.

scholarly journals Hybrid Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of HIV-1 Integrase/Inhibitor Complexes

2007 ◽  
Vol 93 (10) ◽  
pp. 3613-3626 ◽  
Author(s):  
Nadtanet Nunthaboot ◽  
Somsak Pianwanit ◽  
Vudhichai Parasuk ◽  
Jerry O. Ebalunode ◽  
James M. Briggs ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Integrase Inhibitor ◽  
Quantum Mechanical ◽  
Dynamics Simulations ◽  
Hiv 1
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