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An efficient method for the coordinate transformation problem of massively three-dimensional networks
An efficient method for the coordinate transformation problem of massively three-dimensional networks
- Source :
- The Journal of Chemical Physics. 114:9747-9753
- Publication Year :
- 2001
- Publisher :
- AIP Publishing, 2001.
-
Abstract
- A new and efficient algorithm is presented for the coordinate transformation problem of massively three-dimensional networks formed, e.g., by the atoms of crystal fragments or molecular clusters. The new algorithm is based on a divide-and-conquer technique to perform iterative coordinate transformation, applicable even for three-dimensional networks, with linear scaling memory and near linear scaling CPU time requirements. The new algorithm proved to be very fast in the coordinate transformation problems and geometry optimization of diamond fragments, water clusters, globular proteins, and proteins in solvent.
- Subjects :
- chemistry.chemical_classification
010304 chemical physics
Computer science
Globular protein
Coordinate system
Molecular biophysics
General Physics and Astronomy
CPU time
010402 general chemistry
Energy minimization
01 natural sciences
0104 chemical sciences
Computational science
Crystal (programming language)
chemistry
Computational chemistry
0103 physical sciences
Linear scale
Energy level
Physical and Theoretical Chemistry
Subjects
Details
- ISSN :
- 10897690 and 00219606
- Volume :
- 114
- Database :
- OpenAIRE
- Journal :
- The Journal of Chemical Physics
- Accession number :
- edsair.doi...........1a519496255d8d7bfc91a87ba0fe775c
- Full Text :
- https://doi.org/10.1063/1.1370534