I first had to run a molecular dynamics simulation (via. workshop 1) to visualize the protein Influenza Neuraminidase 3BEQ. But before you can run a molecular dynamics simulation, you must know how to set up the simulation. Setting up the simulation and running the simulation wasn’t too bad. There is a learning curve when learning how to set up and run these simulations. All the errors I made when first trying to set up and run the simulation only helped me become better at the process.
I then had to run a molecular dynamics simulation (via workshop 2) to get the energy minimization and equilibration for the protein Influenza Neuraminidase 3BEQ. First time trying to run this simulation I encountered a road block, which was my own typos. Outside of the typos and making sure the input was perfect, I believe running these simulations was also not too bad. Errors also made me better at running this simulation.
Running these simulations through Putty introduced me to vim, which is a text editor. Vim allows you to edit a file in Putty. Learning Vim was not too bad also because of the Vim tutor that vim has. It teaches you the basics and everything I needed to know to successfully run the simulations.
The biggest thing I had to overcomer, for me, was to learn all these new features and remember how to use them. But once I surpassed the learning curve, It became progressively easier to get through the simulations.
You’re trying to cover a LOT of material in just one post, which makes it less effective. Consider splitting this into several blog posts, and flesh out each one with a few details and commands that would be useful for a reader.
1) One post with a high-level overview of the MD simulation process and AMBER. Mention each stage of the process, what the end goal is, etc. Link to https://en.wikipedia.org/wiki/Viral_neuraminidase and any other relevant webpages.
2) One post on what you needed to learn to access comet: putty/winscp, basic linux commands you found most useful (you can always update these posts as you learn more)
3) One post on vi/vim would be good. Discuss why you need it, what makes it powerful, basic commands you found useful, and yes, mention vim tutor!