Substructured multibody molecular dynamics.

Technical Report · Wed Nov 01 04:00:00 EST 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
• Sponsoring Organization: USDOE
• DOE Contract Number: AC04-94AL85000
• OSTI ID: 902881
• Report Number(s): SAND2006-7085
• Country of Publication: United States
• Language: English

Related Subjects

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