Efficient “Middle” Thermostat Scheme for the Quantum/Classical Canonical Ensemble via Molecular Dynamics

2020 ◽  
pp. 257-281
Author(s):  
Xinzijian Liu ◽  
Kangyu Yan ◽  
Jian Liu
Keyword(s):  
Molecular Dynamics ◽  
Canonical Ensemble

THE "FOLDING" BEHAVIORS OF HOMOPOLYMERS WITH ONE END FIXED

2004 ◽  
Vol 18 (15) ◽  
pp. 2123-2139 ◽  
Author(s):  
BIN XUE ◽  
JUN WANG ◽  
WEI WANG
Keyword(s):  
Molecular Dynamics ◽  
Chain Length ◽  
Conformational Changes ◽  
Canonical Ensemble ◽  
Interaction Strength ◽  
Simulation Method ◽  
Dynamics Simulation ◽  
Radius Of Gyration ◽  
Native Conformation ◽  
Collapse Temperature

We study the "folding" behaviors of homopolymers with one end fixed. By using canonical ensemble molecular dynamics simulation method, we observe the conformational changes during folding processes. Long chains collapse to the helical nuclei, then regroup to helix from the free-end to form the compact conformations through the middle stages of helix-like coil and helix-like cone, while short chains do not apparently have the above mentioned middle stages. Through simulated annealing, the native conformation of homopolymer chain in our model is found to be helix. We show the relations between specific heat C v (T) and radius of gyration R g (T) as functions of temperature, chain length and the interaction strength, respectively. We find that these two quantities match well and can be combined to interpret the "folding" process of the homopolymer. It is found that the collapse temperature Tθ and the native-like folding temperature T f do not change with the chain length in our model, however the interaction strength affects the values of Tθ and T f .

QUASI SYMPLECTIC INTEGRATORS: AN ALTERNATIVE TO NOSÉ HOOVER DYNAMICS?

2005 ◽  
Vol 05 (02) ◽  
pp. L225-L232
Author(s):  
RICCARDO MANNELLA
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Numerical Integration ◽  
Canonical Ensemble ◽  
Symplectic Integrators ◽  
Langevin Equations ◽  
Dynamics Simulations

Quasi symplectic algorithms for the numerical integration of Langevin equations describing systems in a canonical ensemble are discussed. It is shown that they could be an alternative to molecular dynamics simulations done with a Nosé Hoover booster.

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