Grid-based dynamic electronic publication: A case study using combined experiment and simulation studies of crown ethers at the air/water interface.
Esther R Rousay, Hongchen Fu, Jamie M Robinson, Jeremy G Frey, Jonathan W Essex
School of Chemistry, University of Southampton,
Highfield, Southampton, SO17 1BJ, UK

Abstract The Publication@Source Paradigm and Challenges Body Molecular Dynamics Simulations Comparisons and Conclusions Acknowledgements Appendix:The TriScapeRDF browser References Glossary Search
Introduction Introduction - Compute Facility Figures Density Profiles Orientational Distribution

Introduction

To further elucidate the situation at the solution/air interface, a molecular dynamics simulation has been performed. The simulation was carried out using the NAMD package23, which was developed by the Theoretical Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign, and the AMBER99 24 force field. A switching function was applied to the Lennard-Jones interactions between 9 and 11 ? and a time-step of 2.0 fs was employed. The lengths of bonds containing hydrogen were constrained using the SHAKE25 algorithm. The long-range interactions are treated using the particle mesh Ewald technique26 with an interpolation parameter of 6 ? -1. Periodic boundary conditions were applied in all directions, and the simulation was carried out at 298K. An SPC/E27 water box of dimensions 80 ? ? 80 ? ? 60 ? was minimised, heated gradually from 100 K to 298 K under NVT conditions using a Langevin thermostat28 with damping parameter 10 ps-1, and then equilibrated in a tight NPT ensemble for 0.1 ns (50000 steps). For this, a Nos?-Hoover Langevin piston barostat29 was used, with a piston temperature of 300 K, a target pressure of 1 atm, an oscillation period of 200 fs, and a decay of 100 fs. The thermostat damping parameter was 10 ps-1. A further 0.4 ns of equilibration was carried out in a loose NPT ensemble. For this, the barostat had an oscillation period of 400 fs and a decay of 300 fs. The thermostat damping parameter was 1 ps-1

The z-axis of the simulation cell was then extended in both directions, such that a central lamellar of water was created, in the manner of Alejandre et al 30. The simulation cell then has dimensions 80 ? ? 80 ? ? 300 ?. This system was equilibrated under NVT conditions for 0.5 ns, with a damping parameter of 1 ps-1, and the z-profile of the system was monitored to check that the slab was stable (figure 10). The crown ether molecule was built from its crystal structure31. Charges were generated using the RESP method32 which employs the HF 6-31G* basis set. This structure was minimised in the gas phase using molecular mechanics, and one, minimised crown ether, was lowered onto each interface of the slab until in close proximity to the water. This was done using the XLEAP module of AMBER. Once on the water surface the crown ethers were minimised, whilst the water was fixed, for 10000 steps. The entire system was then equilibrated under constant NVT for 0.5 ns using a thermostat damping parameter of 1 ps-1. 10 ns of production were then run (100 blocks of 50000 steps) under NVT conditions, again with a thermostat damping parameter of 1 ps-1. A representation of the initial simulation cell is shown in Figure 10.

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