Day 2
Plans for Day 2
Unfortunately, last meeting we had some technical difficulties that kept us from completing everything we had set out to. Namely, at the beginning of Day 1 we were not able to successfully set-up OSC accounts for everyone. As of now, an account should have been created for everyone. You may just need to create a password which I can help with. If you do not know your username, please let me know. To reset (or in this case create) your password, go to the OSC Client Portal and click "Forgot your password?".
The other technical issue was related to the permissions of my Gromacs force field directory which kept most of the class from being able to set-up their simulations. I have now copied the directory directly to our scratch space, updated the group, and updated the permissions. I am confident now that it will work. Before we proceed, if you created a directory in our scratch space yesterday, please delete it. The command is "rm -r name", where "name" is the name of your directory. If you created a directory using Luciano's account, Luciano will need to delete it.
Then to proceed, please have a look at the material from "OSC Resources" and "Submitting Our First Job!" from the Day 1 page. Toward the end of the workshop, after the discussion in our presentation (below) and reviewing the content of our input files, we will submit our first free energy calculations. This material can be found in the section "Submitting Your First Solvation Free Energy Calculation", also on the Day 1 page. Know that it may be that your water equilibration has not completed at this time. No worries, we can submit jobs for those systems that have equilibrated.
A copy of my presentation from today is provided below. For Day 2 there will not be a screen cast. The "theory" slides will be covered in the screen cast for my Day 1 presentation.
Summary of Status After Day 2
Today went much better! Today we were able to walk through getting our simulations set-up and running for our equilibration runs. Tomorrow we will pick-up here and submit our free energy calculations, review some concepts from our presentation on Day 1, and the review our input files.