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Install IQmol and connect to Q-Chem

Guide 1 · about 15 minutes, once per semester

All calculations in this lab run in Q-Chem  [1], a professional quantum-chemistry program. You won’t install Q-Chem on your laptop. Instead you’ll use IQmol  [2], a free graphical program that builds the molecule, writes the Q-Chem input and sends the job to a remote server where Q-Chem actually runs. When the job finishes, IQmol brings the results back.

This is how research computing works: you prepare jobs on your own computer, submit them to a shared machine, and analyze the output when it comes back.

 your laptop                         the Q-Chem server
 ┌─────────────────┐   submit job    ┌──────────────────────┐
 │ IQmol           │ ──────────────▶ │ queue → Q-Chem runs  │
 │ (build, set up, │                 │ (≤ 10 min per job)   │
 │  analyze)       │ ◀────────────── │ output file          │
 └─────────────────┘  results back   └──────────────────────┘

1. Install IQmol

  1. Go to iqmol.org and open the Downloads page.
  2. Download the installer for your operating system (Windows, macOS or Linux).
  3. Install it like any other application.
    • macOS: if the system says the app “cannot be opened because the developer cannot be verified”, right-click (or Control-click) IQmol in Applications, choose Open, then confirm. You only need to do this the first time.
    • Windows: if SmartScreen warns you, click More info → Run anyway.
  4. Launch IQmol. You should see an empty 3D viewer with a toolbar on top.
Note

The Florida Tech computer labs may already have IQmol installed. Ask your instructor which rooms.

2. Connect to the free Q-Chem server

IQmol ships with access to a free Q-Chem server for teaching and small calculations.

  1. Open any molecule (for example, download one .xyz file from Experiment 1 and use File → Open).
  2. Open the Q-Chem setup window (Calculation → Q-Chem Setup, or the Q-Chem button on the toolbar).
  3. In the Server menu at the bottom of the window, select the default free Q-Chem server.
  4. The first time, IQmol may ask you to register or accept the server’s terms. Follow the prompts and use your Florida Tech e-mail.
ImportantThe 10-minute rule

Jobs on the free server are stopped after 10 minutes of run time. Everything in Experiments 1–9 is designed to fit, and every experiment page flags the jobs that might be close to the limit. If a job is killed, it is almost always because of a typo in the basis set or method (for example, a much larger basis than intended). See Working on a shared machine.

3. Check that everything works

Run the test job in the first-job guide: one HCl molecule with HF/def2-SVP. It should finish in a few seconds. If it does, you are ready for the experiments.

Troubleshooting

Problem What to try
IQmol won’t start on macOS Right-click → Open (see above). On Apple-silicon Macs, make sure you downloaded the current version.
The server list is empty Check your internet connection and any firewall or VPN. On campus Wi-Fi it should work out of the box.
A job stays “queued” for a long time The server is shared; at busy times (the night before a deadline!) jobs wait. Submit early.
The job fails immediately Open the output file and read the last lines; there is usually a clear error message. Common culprits: wrong charge or multiplicity, or a misspelled basis set.
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References

[1]
E. Epifanovsky et al., Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package, J. Chem. Phys. 155, 084801 (2021).
[2]
A. T. B. Gilbert, IQmol molecular viewer, (n.d.).