Surface Tension Evaluation of Lennard-Jones Fluid System With Untruncated Potentials

Author(s):  
Shashank Sinha ◽  
Vijay K. Dhir ◽  
Bo Shi ◽  
Jonathan B. Freund ◽  
Eric Darve

In typical atomistic simulations of simple liquids, the Lennard-Jones interatomic pair potential is truncated so that algorithms scale as Natoms rather Natoms2, which would be the case if an interaction were computed explicitly for all atom pairs. However, it is known that interfacial properties are sensitive to the cutoff radius selected. Corrections for the missing ‘tails’ of the potential can reduce the error, but cannot eliminate it because the liquid and vapor densities are also sensitive to the cutoff radius. In light of this, we have developed and implemented a NlogN particle-particle particle-mesh (P3M) algorithm to evaluate the 1/r6 dispersive forces between Lennard-Jones fluid molecules without truncation. Statistical expression for the surface tension also scale as N2 if potentials are not truncated, so we also developed a P3M formulation for computing surface tension. The techniques are demonstrated on a thin liquid film suspended in equilibrium with its own vapor. Simulations at several temperatures between the triple point and the critical point are compared with the available data. The expense of the algorithm is competitive for simple geometries and seems preferable in non-trivial geometries without the possibility of tail corrections.

1986 ◽  
Vol 64 (2) ◽  
pp. 211-214
Author(s):  
S. K. Datta

Closed analytical expressions for the diffusion coefficient and shear-viscosity coefficient of dense, simple fluids characterized by the Lennard-Jones potential function have been obtained using the Weeks, Chandler, and Andersen criterion for the division of the pair potential. The expressions are then used to calculate these properties for some real fluids. The deviations between the estimated and measured values of the coefficients are attributed mostly to the approximate nature of the Kirkwood and Rice expressions for shear viscosity and the friction coefficient used to calculate those properties.


Author(s):  
Ian A. Cosden ◽  
Jennifer R. Lukes

Molecular dynamics (MD) simulations are carried out to calculate the surface tension of bubbles formed in a metastable Lennard-Jones (LJ) fluid. The calculated normal and transverse pressure components are used to compute a surface tension which is compared to the surface tension computed from the Young-Laplace equation. Curvature effects on surface tension are investigated by performing various sized simulations ranging from 6,912 to 256,000 LJ particles. Density profiles, pressures, and calculated surface tension are shown to have a strong dependence on the choice of the interaction cutoff radius. A cutoff radius of 8σ, significantly larger than that commonly used in the literature, is recommended for accurate calculations in liquid-vapor systems.


Author(s):  
Jun Pei ◽  
Zheng Zheng ◽  
Hyunji Kim ◽  
Lin Song ◽  
Sarah Walworth ◽  
...  

An accurate scoring function is expected to correctly select the most stable structure from a set of pose candidates. One can hypothesize that a scoring function’s ability to identify the most stable structure might be improved by emphasizing the most relevant atom pairwise interactions. However, it is hard to evaluate the relevant importance for each atom pair using traditional means. With the introduction of machine learning methods, it has become possible to determine the relative importance for each atom pair present in a scoring function. In this work, we use the Random Forest (RF) method to refine a pair potential developed by our laboratory (GARF6) by identifying relevant atom pairs that optimize the performance of the potential on our given task. Our goal is to construct a machine learning (ML) model that can accurately differentiate the native ligand binding pose from candidate poses using a potential refined by RF optimization. We successfully constructed RF models on an unbalanced data set with the ‘comparison’ concept and, the resultant RF models were tested on CASF-2013.5 In a comparison of the performance of our RF models against 29 scoring functions, we found our models outperformed the other scoring functions in predicting the native pose. In addition, we used two artificial designed potential models to address the importance of the GARF potential in the RF models: (1) a scrambled probability function set, which was obtained by mixing up atom pairs and probability functions in GARF, and (2) a uniform probability function set, which share the same peak positions with GARF but have fixed peak heights. The results of accuracy comparison from RF models based on the scrambled, uniform, and original GARF potential clearly showed that the peak positions in the GARF potential are important while the well depths are not. <br>


2000 ◽  
Vol 633 ◽  
Author(s):  
Boris Ni ◽  
Susan B. Sinnott

AbstractAtomistic simulations are used to better understand the behavior of bundles of single- walled carbon nanotubes that have been placed between two sliding diamond surfaces. A many-body reactive empirical potential for hydrocarbons that has been coupled to a Lennard-Jones potential is used to determine the energies and forces for all the atoms in the simulations. The results indicate that the degree of compression of the nanotube bundle between the nanotubes has a significant effect on the responses of the nanotubes to shear forces. However, no rolling of the nanotubes is predicted in contrast to previous studies of individual nanotubes moving on graphite.


2017 ◽  
Vol 147 (8) ◽  
pp. 084902 ◽  
Author(s):  
Siddharth Paliwal ◽  
Vasileios Prymidis ◽  
Laura Filion ◽  
Marjolein Dijkstra

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