Day 1

OSC Resources

All of the calculations in this workshop will be performed on the Ohio Supercomputer Center (OSC). I plan to use OSC OnDemand in this course, which will allow you to connect to the supercomputer using a web browser. In addition to the convenience of connecting via a web browser, it will ensure we are all able to connect to the necessary resources without installing any additional software, and your experience will be the same regardless of the computer you are using. If you forget your username, please let me know. If you forget your password, go to the OSC Client Portal and click "Forgot your password?".

OSC's homepage is full of useful information. Below I will list a few useful pages. If any other useful resources come up during the workshop, we can list them here and along with the relevant material.

    • OSC has a very nice "Getting Started Guide." When you connect to the supercomputer, you will be using a Linux terminal. If you have never used Linux before, you will find the "Unix Basics" information useful. And no worries, when we perform exercises in class I will be there the entire time to help. To be honest, most of my Linux knowledge I just learned by doing.

      • As a note on Linux commands, I exclusively use a "Bash" shell. It is just what I have always used. When you create your OSC account by following the instructions in the e-mail you received from OSC, please be sure to leave your shell as the default Bash type. I do not know if Bash is any better than the others, it is just the default and what I am comfortable using.

    • OSC has a useful page "Batch Processing at OSC." Among other topics, it provides information about loading and unload modules (i.e., software packages) and submitting jobs.

    • OSC has a very nice "OnDemand" page, which provides an overview of connecting to and the features of OSC OnDemand. Their posted video is from 2017; OSC OnDemand looks slightly different now and the Pitzer Cluster that we will use was not yet available. For that reason I have recorded a very short screen cast below which demonstrates my logging into OSC OnDemand and connecting to the Pitzer Cluster.

Submitting Your First Job!

Once we make sure everyone can connect to OSC, we will submit your first calculations! Before we can perform free energy calculations, we need to equilibrate our systems. We will go through the process of equilibrating our systems today. Then at the end of today or tomorrow morning we will submit our first free energy calculations. Ideally I would have liked to have our discussion on free energy calculations first. However, given our limited time, I want to submit our equilibration jobs as soon as possible as our ability to run solvation free energy calculations will be dependent on them. Below is a screen cast wherein I walk you though how to equilibrate our systems.

All of the Gromacs files used may be found in the two Google Drive folders below. This includes the files for the corresponding solvation free energy calculations. If you are participating in the workshop, you do not need to download the files. I already have copies on OSC for you to use. This is intended for your future reference after the workshop is complete.

Theory Behind Solvation Free Energy Calculations Using Molecular Simulation

We will start by discussing the theory behind (equilibrium) perturbative methods to compute the solvation free energy using molecular simulation. Know that only a brief discussion will be presented due to the limited time of the scheduled workshop, which I believe will be sufficient to get you up and running. I will point you to additional references for further study if you are interested. I emphasize that our focus will be on gaining a working knowledge of solvation free energy calculations; we will not go into detail about molecular simulations (molecular dynamics and Monte Carlo). In this workshop we will ultimately using molecular dynamics to sample configurational phase space, using the freely available software package Gromacs. In addition to being freely available, Gromacs is incredibly fast, user friendly, provides excellent documentation, and is under active development. In past releases of Gromacs, they would provide a PDF manual that I would compare to an introductory textbook (see here). Also, given the large user base, many excellent resources and tutorials are available.

Submitting Your First Solvation Free Energy Calculation

Before the end of the day, it would be ideal if we could submit our first solvation free energy calculation. At this point, I will guide you through how to set-up and submit the necessary jobs. Tomorrow we will go over the input files and set-up in detail, and then also discuss analyzing the results. If you are participating in the workshop, copies of the necessary files are available on OSC. But for your future reference, copies may also be found in the Google Drive folders references in "Submitting Your First Job!" Below is a screen cast wherein I walk you though how to set-up and submit our free energy calculations. If the set-up script fails, then there is likely something wrong with your equilibration runs that needs to be investigate. For our workshop, I do not expect any issues.

Summary of Status After Day 1

Unfortunately we were not able to complete everything I had originally planned for Day 1. But no worries, we still have 3 more days which I am confident will be excellent! We ran into issues with permissions getting our equilibration simulations set-up, and there were still issues getting OSC accounts created for everyone. But now before Day 2, accounts have successfully been created for everyone, and I have copies my force field directory directly to our scratch space, and updated the group and permissions. I am confident now that we can get all of our simulations set-up and submitted.