Your first Q-Chem job

Guide 2 · from an .xyz file to a total energy in five minutes

We’ll compute the energy of one HCl molecule with Hartree–Fock and the def2-SVP basis set. Every job in this lab follows the same pattern.

Step 1 · Get the geometry

Download 37_HCl_NCCE30.xyz from the molecule gallery of Experiment 1. Open it in a text editor and you’ll see the format:

2                      ← number of atoms
0 1                    ← charge and spin multiplicity
Cl    0.00   0.00   0.00   ← element and x, y, z in Ångström
H     0.00   0.00   1.28

Note

Standard .xyz files use the second line as a free comment. In this lab we always put the charge and the spin multiplicity (2S+1) there, so you never have to guess them: 1 = singlet (all electrons paired), 2 = doublet (one unpaired electron, e.g. a radical or an H atom), 3 = triplet (e.g. O₂ or the O atom), and so on.

Step 2 · Open it in IQmol

File → Open and choose the .xyz file. The molecule appears in the 3D viewer; drag to rotate it, scroll to zoom.

Step 3 · Set up the calculation

Open Calculation → Q-Chem Setup. You have two equivalent options.

Option A: fill in the setup window. Set:

Field	Value for this test
Calculation (job type)	Energy (single point)
Method	HF
Basis	def2-SVP
Charge / Multiplicity	0 / 1

Option B: paste a ready-made input. Every experiment page has a Run the calculations section with the complete Q-Chem input for each job. Click Copy input and paste it into IQmol’s input editor (the text preview of the input in the setup window), replacing what is there. For this test it is:

$molecule
0 1
Cl     0.00000000     0.00000000     0.00000000
H      0.00000000     0.00000000     1.27907000
$end

$rem
   JOBTYPE              SP
   METHOD               HF
   BASIS                def2-SVP
   SCF_CONVERGENCE      8
$end

The $molecule block holds charge, multiplicity and coordinates. The $rem block holds the instructions: JOBTYPE SP is a single-point energy, METHOD the functional (or HF), BASIS the basis set, and SCF_CONVERGENCE 8 asks for tight convergence (energy changes below 10⁻⁸).

Name your jobs systematically

Give every job a name that says what it is, e.g. ex01_hf_def2-svp_hcl. You’ll run hundreds of jobs this semester; good names save hours. The input generator on each experiment page already uses this convention.

Step 4 · Submit

Choose the free Q-Chem server in the Server menu, give the job a name, and click Submit. IQmol opens the Job Monitor, where you can follow the job: queued → running → finished.

Step 5 · Get the result

When the job finishes, IQmol copies the results back. Open the output file (the job’s .out file; in the Job Monitor you can open or save the job’s output). Everything you need is in that text file; Guide 3 shows exactly where. For this test job, look for the line

 Total energy in the final basis set =     -4xx.xxxxxxxxxx

A number close to −460 hartree means everything works. 🎉

Keep your output files

Save every output file in an organized folder (one folder per experiment). If a number looks strange later, the output is the only way to find out why.