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Title: Substructured multibody molecular dynamics.

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.
Authors:
; ; ;  [1] ; ; ; ;  [2] ;
  1. (Johns Hopkins University, Baltimore, MD)
  2. (Rensselaer Polytechnic Institute, Troy, NY)
Publication Date:
OSTI Identifier:
902881
Report Number(s):
SAND2006-7085
TRN: US200720%%240
DOE Contract Number:
AC04-94AL85000
Resource Type:
Technical Report
Research Org:
Sandia National Laboratories
Sponsoring Org:
USDOE
Country of Publication:
United States
Language:
English
Subject:
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.