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Molecular Dynamics
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Molecular Dynamics


Molecular Dynamics
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1.  Looking for Molecular Dynamics open in new window
We have reviewed and sorted 463 odd links for molecular dynamics - the top 10 list is presented here..
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2.  Molecular Dynamics open in new window
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CHARMM. Molecular Dynamics Simulations open in new window
Introduction with applications through the CHARMM program.
(http://www.ch.embnet.org/MD_tutorial/)

Home page - Dennis Rapaport open in new window
Sections on molecular dynamics include java simulations, visualization and interactivity.
(http://www.ph.biu.ac.il/~rapaport/)

Introduction to molecular dynamics simulations. Overheads of the lecture (html version). open in new window
Overview of key ideas through journal article clippings and lecture notes.
(http://www.unizh.ch/~bioinfo/WS02_03/AC/lecture_cell_net_and)

MD Engine II PC open in new window
MD Engine II PC from Fuji Xerox is a high performance accelerator board for the PC that dramatically increases the speed of molecular dynamic simulations. Distributed by CONFLEX Corporation.
(http://md-engine.conflex.us/)

MD simulations of actin open in new window
Simulations on Mg and Ca-bound actin, water diffusion pathways and monomer interactions in F-actin.
(http://yakko.bme.virginia.edu/cm/test.html)

Molecular Dynamics open in new window
A tutorial published by the Center for Molecular Modeling of the U.S. National Institutes of Health.
(http://cmm.info.nih.gov/modeling/guide_documents/molecular_d)

Molecular Dynamics open in new window
Includes an extensive tutorial, with sample programs in Fortran 90, and links to software packages.
(http://www.fisica.uniud.it/~ercolessi/md/)

Molecular Dynamics open in new window
Focuses on parallel molecular dynamics: algorithms, benchmark timings, codes and simulation results. Includes several article references.
(http://www.cs.sandia.gov/~sjplimp/md.html)

Molecular Dynamics Simulations of Polymers: An Introduction open in new window
Introduction with emphasis on polymer applications; powerpoint presentation.
(http://www.che.utah.edu/~gdsmith/tutorials/tutorial1.ppt)

NAMD Scalable Molecular Dynamics open in new window
NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems.
(http://www.ks.uiuc.edu/Research/namd/)

NWChem High Performance Computational Chemistry Software open in new window
NWChem is a computational chemistry software capable of molecular dynamics simulations. It is designed to run on parallel computers and it is developed by the Pacific Northwest National Laboratory.
(http://www.emsl.pnl.gov:2080/docs/nwchem/nwchem.html)

Topics on Protein Dynamics open in new window
Includes sections on molecular dynamics: introduction, advanced topics and output analysis.
(http://www.orcero.org/irbis/md/)


Molecular Dynamics
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