Name
Abstract | ||
|---|---|---|
We present an order N method for calculating electrostatic interactions that has been integrated into the molecular dynamics portion of the TINKER Molecular Modeling package. This method, introduced in a previous paper [Y. Lin, A. Baumketner, S. Deng, Z. Xu, D. Jacobs, W. Cai, An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions, J. Chem. Phys. 131 (2009) 154103] and termed the Image-Charge Solvation Model (ICSM), is a hybrid electrostatic approach that combines the strengths of both explicit and implicit representations of the solvent. A multiple-image method is used to calculate reaction fields due to the implicit part while the Fast Multipole Method (FMM) is used to calculate the Coulomb interactions for all charges, including the explicit part. The integrated package is validated through test simulations of liquid water. The results are compared with those obtained by the Particle Mesh Ewald (PME) method that is built in the TINKER package. Timing performance of TINKER with the integrated ICSM is benchmarked on bulk water as a function of the size of the system. In particular, timing analysis results show that the ICSM outperforms the PME for sufficiently large systems with the break-even point at around 30,000 particles in the simulated system. |
Year | DOI | Venue |
|---|---|---|
2013 | 10.1016/j.cpc.2012.08.003 | Computer Physics Communications |
Keywords | Field | DocType |
Method of images,Reaction field,Electrostatic interaction,TINKER | Statistical physics,Coulomb,Electrostatics,Particle Mesh,Mathematical analysis,Operations research,Static timing analysis,Molecular dynamics,Solvation,Fast multipole method,Mathematics,Method of images | Journal |
Volume | Issue | ISSN |
184 | 1 | 0010-4655 |
Citations | PageRank | References |
2 | 0.39 | 5 |
Authors | ||
6 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Katherine Baker | 1 | 2 | 0.39 |
| Andrij Baumketner | 2 | 6 | 1.23 |
| Yuchun Lin | 3 | 4 | 1.24 |
| Shaozhong Deng | 4 | 44 | 8.78 |
| Donald Jacobs | 5 | 38 | 4.07 |
| Wei Cai | 6 | 2 | 0.39 |