Substructured multibody molecular dynamics.

Technical Report · 01 November 2006

DOI:https://doi.org/10.2172/902881· OSTI ID:902881

Grest, Gary Stephen; Stevens, Mark Jackson; Plimpton, Steven James; Woolf, Thomas B ^[1]; Lehoucq, Richard B; Crozier, Paul Stewart; Ismail, Ahmed E; Mukherjee, Rudranarayan M ^[2]; Draganescu, Andrei I

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1. Johns Hopkins University, Baltimore, MD
2. Rensselaer Polytechnic Institute, Troy, NY

We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

• Research Organization: Sandia National Laboratories (SNL), Albuquerque, NM, and Livermore, CA (United States)
• Sponsoring Organization: USDOE
• DOE Contract Number: AC04-94AL85000
• OSTI ID: 902881
• Report Number(s): SAND2006-7085; TRN: US200720%%240
• Country of Publication: United States
• Language: English

Related Subjects

99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE
MOLECULAR DYNAMICS METHOD
L CODES
RHODOPSIN
ISOMERIZATION
SURFACE TENSION
WATER
Molecular dynamics-Computer simulation.
Molecular dynamics-Simulation methods.
Parallel processing (Electronic computers)
Simulation methods.