A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen-like peptides

2005 ◽  
Vol 26 (15) ◽  
pp. 1612-1616 ◽  
Author(s):  
Sanghyun Park ◽  
Randall J. Radmer ◽  
Teri E. Klein ◽  
Vijay S. Pande
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Mechanics ◽  
Dynamics Simulations

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.

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