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Title: Substructured multibody molecular dynamics.

Abstract

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:
Research Org.:
Sandia National Laboratories
Sponsoring Org.:
USDOE
OSTI Identifier:
902881
Report Number(s):
SAND2006-7085
TRN: US200720%%240
DOE Contract Number:
AC04-94AL85000
Resource Type:
Technical Report
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.

Citation Formats

Grest, Gary Stephen, Stevens, Mark Jackson, Plimpton, Steven James, Woolf, Thomas B., Lehoucq, Richard B., Crozier, Paul Stewart, Ismail, Ahmed E., Mukherjee, Rudranarayan M., and Draganescu, Andrei I. Substructured multibody molecular dynamics.. United States: N. p., 2006. Web. doi:10.2172/902881.
Grest, Gary Stephen, Stevens, Mark Jackson, Plimpton, Steven James, Woolf, Thomas B., Lehoucq, Richard B., Crozier, Paul Stewart, Ismail, Ahmed E., Mukherjee, Rudranarayan M., & Draganescu, Andrei I. Substructured multibody molecular dynamics.. United States. doi:10.2172/902881.
Grest, Gary Stephen, Stevens, Mark Jackson, Plimpton, Steven James, Woolf, Thomas B., Lehoucq, Richard B., Crozier, Paul Stewart, Ismail, Ahmed E., Mukherjee, Rudranarayan M., and Draganescu, Andrei I. Wed . "Substructured multibody molecular dynamics.". United States. doi:10.2172/902881. https://www.osti.gov/servlets/purl/902881.
@article{osti_902881,
title = {Substructured multibody molecular dynamics.},
author = {Grest, Gary Stephen and Stevens, Mark Jackson and Plimpton, Steven James and Woolf, Thomas B. and Lehoucq, Richard B. and Crozier, Paul Stewart and Ismail, Ahmed E. and Mukherjee, Rudranarayan M. and Draganescu, Andrei I.},
abstractNote = {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.},
doi = {10.2172/902881},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Wed Nov 01 00:00:00 EST 2006},
month = {Wed Nov 01 00:00:00 EST 2006}
}

Technical Report:

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