![enter image description here][1] [Image Source][2] GROMACS tutorial ---------------- [Learn More][3] - GROMACS is the program used to run molecular dynamics simulations. During this tutorial, make sure you take note of *what* each command does rather. best practices are to record every command entered so that someone else could look and the notes and recreate the system. - Have a protein in solution? Need to equilibrate a protein before you do something else to it? Always start at the lysozyme in water tutorial. Complete the lysozyme in water [tutorial][4], write down what every command does after looking it up in the GROMACS user manual. Test your knowledge by ensuring you know what every command does if asked. - Stop at energy minimization and put your energy graph in your notebook. Write a paragraph on what you *think* you did and how you did it. Schedule a meeting with Dr. Brown to discuss. - If you have extra time, read through Chapter 8 (page 245) of the [Gromacs Manual][5] to determine which analysis might be relevant, and how you could use the commands to perform analysis. Have you defined what your research question is yet? Start working on that now. What might you need to consider? Find analysis metrics that may be necessary or useful in answering your research question. This will be invaluable information as your project progresses. [1]: https://mfr.osf.io/export?url=https://osf.io/r7ady/?action=download&mode=render&direct&public_file=True&initialWidth=828&childId=mfrIframe&parentTitle=OSF%20%7C%20gromacsforwiki.png&parentUrl=https://osf.io/r7ady/&format=2400x2400.jpeg [2]: https://www.nvidia.com/content/dam/en-zz/Solutions/Data-Center/gromacs/GROMACS-Logo.png [3]: http://www.mdtutorials.com/gmx/ [4]: http://www.mdtutorials.com/gmx/lysozyme/index.html [5]: ftp://ftp.gromacs.org/pub/manual/manual-5.0.7.pdf