Abstract
Classical equilibrium molecular dynamics (MD) simulations have been performed to investigate the computational performance of the Simple Point Charge (SPC) and TIP4P water models applied to simulation of methane hydrates, and also of liquid water, on a variety of specialised hardware platforms, in addition to estimation of various equilibrium properties of clathrate hydrates. The FPGA-based accelerator MD-GRAPE 3 was used to accelerate substantially the computation of non-bonded forces, while GPU-based platforms were also used in conjunction with CUDA-enabled versions of the LAMMPS MD software packages to reduce computational time dramatically. The dependence of molecular system size and scaling with number of processors was also investigated. Considering performance relative to power consumption, it is seen that GPU-based computing is quite attractive.
Highlights
Clathrate hydrates are non-stoichiometric crystalline inclusion compounds in which a water host lattice encages small guest atoms or molecules in cavities; the empty lattice is thermodynamically unstable, and its existence is due to hydrogen bond stabilization resulting from the enclathration of the trapped solutes in its cages [1,2]
A relative error tolerance of 10−3 was used for Particle Mesh Ewald (PME) electrostatics in conjunction with molecular dynamics (MD)-GRAPE-3, while this was 10−4 for PPPM
For benchmarks on liquid water, simulations were carried out in the NVT ensemble [17] at 298 K initially, with the thermostat period set to 0.2 ps, to allow for relaxation, prior to NPT simulation at 298 K and 1 bar [16], with thermostat and barostat periods of 0.2 and 0.5 ps, respectively
Summary
Clathrate hydrates are non-stoichiometric crystalline inclusion compounds in which a water host lattice encages small guest atoms or molecules in cavities; the empty lattice is thermodynamically unstable, and its existence is due to hydrogen bond stabilization resulting from the enclathration of the trapped solutes in its cages [1,2]. Molecular dynamics (MD) simulation offers a detailed understanding of underlying molecular mechanisms of hydrate behaviour, and the use of specialised hardware platforms offers obvious potential for the longer timescales required for modelling, e.g., kinetic properties. The kinetic mechanisms of clathrate hydrate crystallisation and dissociation, especially at the molecular level, are understood rather poorly. Theoretical predictions of these rates can differ from experimentally measured rates by at least an order of magnitude [1,2,3,4]; improving the understanding of the underlying mechanisms of hydrate kinetics is desirable in terms of enhancing the viability of large-scale methane production from hydrates [3,4]. One of the goals of this article is to highlight the accelerations possible for calculations on moderate- to medium-scale systems of hydrates, and water, and demonstrate the utility of this for determination of hydrate properties in a routine and power-efficient manner
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
