Methods for performing large-scale parallel Molecular Dynamics(MD) simulations are investigated. A perspective on the field of parallel MD simulations is given. Hardware and software aspects are characterized and the interplay between the two is briefly discussed. A method for performing ab initio MD is described; the method essentially recomputes the interaction potential at each time-step. It has been tested on a system of liquid water by comparing results with other simulation methods and experimental results. Different strategies for parallelization are explored. Furthermore, data-parallel methods for short-range and long-range interactions on massively parallel platforms are described and compared. Next, a method for treating electrostatic interactions in MD simulations is developed. It combines the traditional Ewald summation technique with the nonuniform Fast Fourier transform---ENUF for short. The method scales as N log N, where N is the number of charges in the system. ENUF has a behavior very similar to Ewald summation and can be easily and efficiently implemented in existing simulation programs. Finally, an outlook is given and some directions for further developments are suggested.
| Identifer | oai:union.ndltd.org:UPSALLA1/oai:DiVA.org:su-1008 |
| Date | January 2006 |
| Creators | Hedman, Fredrik |
| Publisher | Stockholms universitet, Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi, Stockholm : Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi |
| Source Sets | DiVA Archive at Upsalla University |
| Language | English |
| Detected Language | English |
| Type | Doctoral thesis, comprehensive summary, info:eu-repo/semantics/doctoralThesis, text |
| Format | application/pdf |
| Rights | info:eu-repo/semantics/openAccess |
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