<p>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. </p><p>A method for performing <i>ab initio </i>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.</p><p>Furthermore, data-parallel methods for short-range and long-range interactions on massively parallel platforms are described and compared. </p><p>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 <i>N log N</i>, where <i>N </i>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.</p><p>Finally, an outlook is given and some directions for further developments are suggested.</p>
| Identifer | oai:union.ndltd.org:UPSALLA/oai:DiVA.org:su-1008 |
| Date | January 2006 |
| Creators | Hedman, Fredrik |
| Publisher | Stockholm University, Department of Physical, Inorganic and Structural Chemistry, 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, text |
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