NAMD2: Greater scalability for parallel molecular dynamics

DOI10.1006/jcph.1999.6201zbMath0948.92004OpenAlexW2103815459MaRDI QIDQ1305980

Attila Gursoy, Milind Bhandarkar, Aritomo Shinozaki, Robert D. Skeel, Neal Krawetz, Klaus Schulten, Laxmikant V. Kalé, Krishnan Varadarajan, James C. Phillips, Robert J. Brunner

Publication date: 22 September 1999

Published in: Journal of Computational Physics (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1006/jcph.1999.6201

zbMATH Keywords

biomolecular systemsNAMD2 program

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Biophysics (92C05) Parallel numerical computation (65Y05) Computational methods for problems pertaining to biology (92-08)

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Uses Software

• NAMD
• PVM
• CHARMM
• CHARM++
• NAMD2
• TK
• VMD

Cites Work

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• RATTLE: A velocity version of the SHAKE algorithm for molecular dynamics calculations
• Comments on P\(^3\)M, FMM, and the Ewald method for large periodic Coulombic systems
• Fast parallel algorithms for short-range molecular dynamics
• A fast algorithm for particle simulations

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