Membrane MD Simulation

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<h2>A Membrane Guide to the Universe</h2> <h2>Assessing Convergence</h2> <blockquote> <p><strong>GridMAT-MD</strong> 1. Download the parallel version of GridMAT-MD from <a href="https://github.com/emptyewer/GridMAT-MD-parallel" rel="nofollow">here</a> and click/read around <a href="https://drive.google.com/open?id=0B2d8Pq0mORNNM0pjWkRLXzNnN1k" rel="nofollow">here</a> for a quick summary of the theory and workflow. For an in-depth discussion with the paper, check it out <a href="http://onlinelibrary.wiley.com/doi/10.1002/jcc.21172/abstract;jsessionid=A6951A8AE1B193B586A89DA5EE39E9CF.f02t02" rel="nofollow">here</a>. 2. You’ll need to align all of the frames to the proper periodic boundary conditions with trjconv, as well as get individual frames for the calculations (area per lipid, bilayer thickness, etc.) over time. These calculations (step 4) take some time -- if you skip 100 frames, you’ll wind up with 1 frame/ns, and this computations will take about 0.067 min/frame with a 32 core machine (1 cascades node). This file MUST be provided to the program as a .gro file. Use trjconv to do this: \ <code>echo 0 0 | $GMX/gmx trjconv -f ../../md_0_200.xtc -s ../../md_0_200.tpr -skip 100 -pbc mol -ur compact -center -o cat_gridmat.gro</code>\ Where md_0_200.xtc is the .xtc file containing the entire trajectory, md_0_200.tpr is the initial tpr file, and cat_gridmat.gro is the output for GridMAT-MD. <a href="https://docs.google.com/document/d/1eFNo7rnOso5zMuK5jYe71sPPap3m65SqTm1TxK47N-E/edit" rel="nofollow">Learn More</a></p> </blockquote>
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