An Effective Genetic-Based Mathematical Computation Algorithm for Minimizing the Lennard-Jones Potential

2011 ◽  
Vol 474-476 ◽  
pp. 2221-2224
Author(s):  
Guo Cheng Li
Keyword(s):  
Molecular Dynamics ◽  
Correct Choice ◽  
Lennard Jones Potential ◽  
Effective Algorithm ◽  
Jones Potential ◽  
Lennard Jones ◽  
Discrete Gradient Method ◽  
Computation Algorithm ◽  
Mathematical Computation ◽  
Present Algorithm

In molecular dynamics, molecular mechanics and quantum mechanics for a complicated system, most of the numerical calculations are at the Lennard-Jones potential. So, effective treatment of Lennard-Jones potential shows an important role. This paper presents an effective algorithm for the optimization of Lennard-Jones potential. The algorithm is a genetic-based algorithm associated with the owerful discrete gradient method and the correct choice of initial coordinates. Numerical results show the effectiveness of the present algorithm and new bestresults for 39,40,42,48,55,75,76,97 atoms were found. These results might be used to study the structure of spherical viruses and molecules.

Surface Tension Evaluation Via Thermodynamic Analysis of Statistical Data From Molecular Dynamics Simulations

Volume 4 ◽  
2004 ◽  
Author(s):  
Aaron P. Wemhoff ◽  
Van P. Carey
Keyword(s):  
Molecular Dynamics ◽  
Surface Tension ◽  
Density Profile ◽  
Md Simulation ◽  
Md Simulations ◽  
Bulk Liquid ◽  
Interfacial Region ◽  
Lennard Jones Potential ◽  
Jones Potential ◽  
Lennard Jones

Surface tension determination of liquid-vapor interfaces of polyatomic fluids using traditional methods has shown to be difficult due to the requirement of evaluating complex intermolecular potentials. However, analytical techniques have recently been developed that determine surface tension solely by means of the characteristics of the interfacial region between the bulk liquid and vapor regions. A post-simulation application of the excess free energy density integration (EFEDI) method was used for analysis of the resultant density profile of molecular dynamics (MD) simulations of argon using a simple Lennard-Jones potential and diatomic nitrogen using a two-center Lennard-Jones potential. MD simulations were also run for an approximation of nitrogen using the simple Lennard-Jones potential. In each MD simulation, a liquid film was initialized between vapor regions and NVE-type simulations were run to equilibrium. The simulation domain was divided into bins across the interfacial region for fluid density collection, and the resultant interfacial region density profile was used for surface tension evaluation. Application of the EFEDI method to these MD simulation results exhibited good approximations to surface tension as a function of temperature for both a simple and complex potential.

Usage of graphics processing units for solving molecular dynamics problems

2011 ◽  
Vol 8 (1) ◽  
pp. 182-188
Author(s):  
D.F. Marin
Keyword(s):  
Molecular Dynamics ◽  
Graphics Processing Units ◽  
Computational Scheme ◽  
Lennard Jones Potential ◽  
Jones Potential ◽  
Lennard Jones ◽  
Graphics Processing ◽  
Dynamics Problems

The paper presents results on performance and efficiency of GPU utilization in a simulation of molecular dynamics processes. The simulation was done with the usage of Lennard-Jones potential and leapfrog computational scheme.

Relativistic Molecular Dynamics Simulations of Laser Ablation Process on the Xenon Solid

2009 ◽  
Vol 131 (3) ◽  
Author(s):  
Yun-Che Wang ◽  
Jing-Wen Chen ◽  
Lun-De Liao ◽  
Hong-Chang Lin ◽  
Chi-Chuan Hwang
Keyword(s):  
Molecular Dynamics ◽  
Laser Ablation ◽  
Special Relativity ◽  
Coulomb Potential ◽  
Charged Particles ◽  
Lennard Jones Potential ◽  
Ablation Process ◽  
Jones Potential ◽  
Lennard Jones ◽  
Laser Ablation Process

The phenomena of Coulomb explosion require the consideration of special relativity due to the involvement of high energy electrons or ions. It is known that laser ablation processes at high laser intensities may lead to the Coulomb explosion, and their released energy is in the regime of kEV to MeV. In contrast to conventional molecular dynamics (MD) simulations, we adopt the three-dimensional relativistic molecular dynamics (RMD) method to consider the effects of special relativity in the conventional MD simulation for charged particles in strong electromagnetic fields. Furthermore, we develop a Coulomb force scheme, combined with the Lennard-Jones potential, to calculate interactions between charged particles, and adopt a Verlet list scheme to compute the interactions between each particle. The energy transfer from the laser pulses to the solid surface is not directly simulated. Instead, we directly assign ion charges to the surface atoms that are illuminated by the laser. By introducing the Coulomb potential into the Lennard-Jones potential, we are able to mimic the laser energy being dumped into the xenon (Xe) solid, and track the motion of each Xe atom. In other words, the laser intensity is simulated by using the repulsive forces from the Coulomb potential. Both nonrelativistic and relativistic simulations are performed, and the RMD method provides more realistic results, in particular, when high-intensity laser is used. In addition, it is found that the damage depth does not increase with repeated laser ablation when the pulse frequency is comparable to the duration of the pulse. Furthermore, we report the time evolution of energy propagation in space in the laser ablation process. The temporal-spatial distribution of energy indirectly indicates the temperature evolution on the surface of the Xe solid under intense laser illumination.

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