scholarly journals New fitting scheme to obtain effective potential from Car-Parrinello molecular-dynamics simulations: Application to silica

2008 ◽  
Vol 82 (1) ◽  
pp. 17001 ◽  
Author(s):  
A. Carré ◽  
J. Horbach ◽  
S. Ispas ◽  
W. Kob
Polymers ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 2659
Author(s):  
Fuchen Guo ◽  
Ke Li ◽  
Jiaxin Wu ◽  
Linli He ◽  
Linxi Zhang

The effects of topological constraints on penetration structures of semi-flexible ring polymers in a melt are investigated using molecular dynamics simulations, considering simultaneously the effects of the chain stiffness. Three topology types of rings are considered: 01-knot (the unknotted), 31-knot and 61-knot ring polymers, respectively. With the improved algorithm to detect and quantify the inter-ring penetration (or inter-ring threading), the degree of ring threading does not increase monotonously with the chain stiffness, existing a peak value at the intermediate stiffness. It indicates that rings interpenetrate most at intermediate stiffness where there is a balance between coil expansion (favoring penetrations) and stiffness (inhibiting penetrations). Meanwhile, the inter-ring penetration would be suppressed with the knot complexity of the rings. The analysis of effective potential between the rings provides a better understanding for this non-monotonous behavior in inter-ring penetration.


2019 ◽  
Vol 18 (02) ◽  
pp. 1940006 ◽  
Author(s):  
M. L. Barabash ◽  
W. A. T. Gibby ◽  
C. Guardiani ◽  
D. G. Luchinsky ◽  
P. V. E. McClintock

We consider the selective permeation of ions through narrow water-filled channels in the presence of strong interaction between the ions. These interactions lead to highly correlated ionic motion, which can conveniently be described via the concept of a quasiparticle. Here, we connect the quasiparticle’s effective potential and the multi-ion potential of the mean force, found through molecular dynamics simulations, and we validate the method on an analytical toy model of the KcsA channel. Possible future applications of the method to the connection between molecular dynamical calculations and the experimentally measured current-voltage and current-concentration characteristics of the channel are discussed.


2015 ◽  
Vol 17 (22) ◽  
pp. 14355-14359 ◽  
Author(s):  
Thomas Spura ◽  
Hossam Elgabarty ◽  
Thomas D. Kühne

“On-the-fly” coupled cluster-based path-integral molecular dynamics simulations predict that the effective potential of the protonated water–dimer has a single-well only.


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