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Algorithms for Molecular Dynamics Simulations
Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
2006 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

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.
Keyword [en]
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
National Category
Physical Chemistry
Identifiers
URN: urn:nbn:se:su:diva-1008ISBN: 91-7155-277-4 (print)OAI: oai:DiVA.org:su-1008DiVA: diva2:189169
Public defence
2006-06-10, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 12 A, Stockholm, 13:00
Opponent
Supervisors
Available from: 2006-05-19 Created: 2006-05-19Bibliographically approved
List of papers
1. A Parallel Quantum Mechanical MD Simulation
Open this publication in new window or tab >>A Parallel Quantum Mechanical MD Simulation
1998 In: Molecular Simulation, ISSN 0892-7022, Vol. 20, no 5, 265-284 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-22612 (URN)
Note
Part of urn:nbn:se:su:diva-1008Available from: 2006-05-19 Created: 2006-05-19Bibliographically approved
2. Parallel aspects of quantum molecular dynamics simulations of liquids
Open this publication in new window or tab >>Parallel aspects of quantum molecular dynamics simulations of liquids
2000 In: Computer Physics Communications, ISSN 0010-4655, Vol. 128, no 1-2, 284-294 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-22613 (URN)
Note
Part of urn:nbn:se:su:diva-1008Available from: 2006-05-19 Created: 2006-05-19Bibliographically approved
3. Data Parallel Large-Scale Molecular Dynamics for Liquids
Open this publication in new window or tab >>Data Parallel Large-Scale Molecular Dynamics for Liquids
1993 In: International Journal of Quantum Chemistry, ISSN 0020-7608, Vol. 46, no 1, 27-38 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-22614 (URN)
Note
Part of urn:nbn:se:su:diva-1008Available from: 2006-05-19 Created: 2006-05-19Bibliographically approved
4. A Data-parallel Molecular Dynamics Method for Liquids with Coulombic Interactions
Open this publication in new window or tab >>A Data-parallel Molecular Dynamics Method for Liquids with Coulombic Interactions
1995 In: Molecular Simulation, ISSN 0892-7022, Vol. 14, no 4-5, 235-244 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-22615 (URN)
Note
Part of urn:nbn:se:su:diva-1008Available from: 2006-05-19 Created: 2006-05-19Bibliographically approved
5. Ewald Summation Based on Nonuniform Fast Fourier Transform
Open this publication in new window or tab >>Ewald Summation Based on Nonuniform Fast Fourier Transform
2006 (English)In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 425, no 1-3, 142-147 p.Article in journal (Refereed) Published
Abstract [en]

We present a novel approach, that combines the traditional Ewald summation technique with the nonuniform Fast Fourier transform to calculate the electrostatic energies and forces in molecular computer simulations. The method can easily be implemented in existing simulation programs. We report here some results from our implementation, where we utilize widely available libraries, and demonstrate the accuracy, and expected computational complexity of our approach.

National Category
Physical Chemistry
Identifiers
urn:nbn:se:su:diva-22616 (URN)10.1016/j.cplett.2006.04.106 (DOI)
Note
Part of urn:nbn:se:su:diva-1008Available from: 2006-05-19 Created: 2006-05-19 Last updated: 2017-12-13Bibliographically approved

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