Molecular Dynamics Simulation

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1. XcelerateAug 2012
   Sure! Checkout LAMMPS (http://lammps.sandia.gov/) and these tutorials https://icme.hpc.msstate.edu/mediawiki/index.php/LAMMPS_tuto...

   Also, check out Molecular Dynamics Simulation (http://www.amazon.com/Molecular-Dynamics-Simulation-Elementa...)

   and Computer Simulation of Liquids (http://www.amazon.com/Computer-Simulation-Liquids-M-Allen/dp...)

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2. kisna72Jun 2020
   Hi,

   I am wondering if anyone has recommendations on resources to learn how to simulate proteins.

   I was having the most interesting conversation about proteins with a friend who is doing her PHD in antibiotics. She told me she had to run a protein simulation, and how her professor sent it over to some lab with super computers. so definitely interested in learning what the state of the art is with regards to these simulations.

   I've done ~4 years of Physics modeling so I am familiar with how simulation in the engineering world works.

   I've done cursory googling and found some books - but looking for recommendations before I make a purchase.

   https://link.springer.com/bookseries/7651 https://www.wiley.com/en-us/Molecular+Dynamics+Simulation%3A+Elementary+Methods-p-9780471184393

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3. Dn_AbJun 2012
   I too was recently looking for how someone with good machine learning experience could contribute. I signed up for the pharma, neurobiology and genomics coursera courses.

   My research also pointed me to the following books. The first two I got because they were highly recommended and most fit my interests.

   Genes, Proteins and Computers

   A Practical Introduction to the Simulation of Molecular Systems

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   ##Ungot

   An Introduction to Bioinformatics Algorithms

   Bioinformatics : Machine learning approaches

   Computational Genome Analysis,

   Understanding Bioinformatics by Marketa Zvelebil

   Biological Sequence Analysis, Durbin et al

   Bioinformatics by David Mount :

   Statistical Methods in Bioinformatics Warren J. Ewens, Gregory R. Grant

   Bioinformatics Basics: Applications in Biological Science and Medicine

   Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison

   Understanding Bioinformatics

   Bioinformatics for Dummies

   Molecular Evolution

   Bioinformatics and Molecular Evolution

   Algorithms on Strings, Tree's and Sequences

   Bioinformatics - A Practical Guide to the analysis of Genes and Protein

   The Art of Molecular Dynamics Simulation

   Protein Bioinformatics: An Algorithmic Approach to Sequence and Structure Analysis

   'Bioinformatics and Functional Genomics

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