Algorithms for Molecular Dynamics Simulations
2006 (English)Doctoral thesis, comprehensive summary (Other academic)
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.
Place, publisher, year, edition, pages
Stockholm: Institutionen för fysikalisk kemi, oorganisk kemi och strukturkemi , 2006. , 93 p.
molecular dynamics, MD, first principles molecular dynamics, quantum mechanics, liquid water, parallel algorithm, data parallel, MPI, Coulombic interaction, Ewald summation, nonuniform fast Fourier transform, FFT, FFTW, NFFT, ENUF
IdentifiersURN: urn:nbn:se:su:diva-1008ISBN: 91-7155-277-4OAI: oai:DiVA.org:su-1008DiVA: diva2:189169
2006-06-10, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 12 A, Stockholm, 13:00
Darden, Tom, Professor
Laaksonen, Aatto, Professor
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