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In this tutorial, we will assign a quantum (QC) region to a system previously prepared in pDynamo using the OPLS force field. The main idea is to select a specific group of atoms of interest and describe them using an electronic structure method, while the remaining atoms continue to be represented by the classical force field. This results in a QC/MM hybrid model, where only the region of interest is treated quantum mechanically, significantly reducing the computational cost compared to a fully quantum calculation.
A more detailed description of the hybrid Hamiltonian implemented in pDynamo, as well as the available quantum methods, can be found here.
1. Opening the System
The first step is to open a system that has already been prepared using the OPLS force field. The corresponding file can be found in the directory:
../EasyHybrid/examples/pkl
which is included with the standard EasyHybrid installation.
After loading the system, observe the status bar located at the bottom of the main window. It indicates that the system is currently described by a purely classical Hamiltonian (OPLS), meaning that no quantum region has been defined yet.
Note: The status bar provides a quick way to verify which Hamiltonian is currently assigned to the system before performing any calculations.
2. Selecting the QC Region
Locate and select the residue TYR2 (Tyrosine 2). You can use the interactive sequence browser available in the tabs located at the bottom of the main window.
Once the residue has been selected, right-click to open the context menu and choose Assign Selection to QC Region (or the equivalent menu option).
This operation tells EasyHybrid that the selected atoms will be described by a quantum mechanical method during subsequent calculations.
3. Configuring the Quantum Region
A dialog window will appear, allowing you to configure the parameters of the QC region. For this tutorial, no changes to the default settings are required. The following parameters will be used:
Quantum method: AM1
Total charge of the QC region: 0
Spin multiplicity: 1 (singlet)
Confirm the settings. If everything is correct, the atoms belonging to the quantum region will automatically be displayed using the Ball and Stick representation, making them easier to identify in the molecular viewer.
Tip: This graphical representation is only intended to highlight the QC region. It does not modify the physical system or affect the calculation itself.
4. Verifying the Hybrid Hamiltonian
After assigning the QC region, look again at the status bar.
It should now indicate that the system is described by a hybrid Hamiltonian combining the AM1 quantum method with the OPLS force field.
From this point onward, any calculation performed—including single-point energy evaluations, geometry optimizations, molecular dynamics simulations, or other sampling procedures—will use the QC/MM hybrid Hamiltonian.
5. Geometry Optimization
In this example, we will perform a geometry optimization.
Click the corresponding toolbar button, as illustrated in the figure. The default settings are sufficient for this tutorial, so no additional modifications are necessary.
Once the optimization has finished, a new set of coordinates will be created automatically. This makes it easy to compare the initial and optimized geometries by displaying both structures simultaneously in the visualization window.
Note: Keeping both structures loaded at the same time provides a convenient way to inspect the structural changes introduced during the optimization.
6. Calculating and Visualizing Molecular Orbitals
In the final step, we will calculate the molecular orbitals for the optimized geometry. From the main menu, select
Analysis → Surfaces
In the dialog window, verify that:
the correct molecular system is selected;
the coordinate set corresponds to the optimized geometry.
Next, click Get Orbitals (this step may take a few seconds)
Once the calculation is complete, the list of molecular orbitals will appear in the object tree within the same window. Select the HOMO, as shown in the figure, and click Render.
EasyHybrid will generate the corresponding molecular orbital surface and automatically associate the resulting volumetric object with the optimized coordinate set.
The generated surface can then be manipulated using the standard visualization tools available in EasyHybrid.
7. Exploring Additional Molecular Orbitals
The same procedure can be used to visualize any other molecular orbital, such as the LUMO, HOMO−1, LUMO+1, or any other orbital listed in the dialog.
Comparing different molecular orbitals can provide valuable insights into chemical bonding, reactive regions, electron transfer processes, and the electronic properties of the quantum region.
Suggestion: Try rendering both the HOMO and the LUMO simultaneously using different colors. Comparing these orbitals often provides a useful first impression of the regions most likely to participate in chemical reactions
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Summary of System "Chignolin (1UAO)"
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-------------------------------------------------- Atoms -------------------------------------------------
Atoms = 138 Heavy Atoms = 77
Hydrogens = 61
---------------------------------------------- Connectivity ----------------------------------------------
Angles = 249 Atoms = 138
Bonds = 141 Dihedrals = 369
Isolates = 1 Ring Sets = 3
-------------------------------------------- Electronic State --------------------------------------------
Electronic Charge = 0 Is Spin Restricted = True
Occupancy Type = Cardinal Spin Multiplicity = 1
------------------------------------------------ Sequence ------------------------------------------------
Atoms = 138 Components = 10
Entities = 1 Linear Polymers = 1
Links = 9 Variants = 4
---------------------------------------------- OPLS MM Model ---------------------------------------------
1-4 Interactions = 353 1-4 Lennard-Jones Form = OPLS
1-4 Lennard-Jones Types = 20 Electrostatic 1-4 Scaling = 0.500
Exclusions = 743 Fourier Dihedral Inactive = 49
Fourier Dihedral Parameters = 101 Fourier Dihedral Terms = 368
Fourier Out-Of-Plane Inactive = 24 Fourier Out-Of-Plane Parameters = 14
Fourier Out-Of-Plane Terms = 108 Harmonic Angle Inactive = 37
Harmonic Angle Parameters = 52 Harmonic Angle Terms = 249
Harmonic Bond Inactive = 21 Harmonic Bond Parameters = 26
Harmonic Bond Terms = 141 Lennard-Jones Form = OPLS
Lennard-Jones Types = 20 Number of MM Atom Types = 20
Number of MM Atoms = 138 Number of Other MM Atoms = 2
Number of Pure MM Atoms = 115 Parameter Set = protein
Total MM Charge = -2.00
---------------------------------------------- MNDO QC Model ---------------------------------------------
Alpha Charge = 32.000 Beta Charge = 32.000
Energy Base Line = 78.971 Exchange Scaling = 1.000
Hamiltonian = am1 MNDO Parameter Entries = 4
Number of Boundary Atoms = 2 Number of QC Atoms = 23
Orbital Basis Functions = 59 Orthogonalization Method = Symmetric
Relative Link Atom Distance = True SCF Converger = DIIS SCF Converger
--------------------------------------------- CutOff NB Model --------------------------------------------
Cell Size = 6.750 CutOff Cell Size Factor = 0.500
Damping Cut-Off = 0.500 Dielectric = 1.000
Grid Cell/Cell Method = True Inner Cut-Off = 8.000
List CutOff = 13.500 Minimum Cell Extent = 2
Minimum Cell Size = 3.000 Minimum Extent Factor = 1.500
Minimum Points = 500 Outer Cut-Off = 12.000
Sort Indices = False Use Centering = True
------------------------------- CutOff Multipole QC/MM Electrostatic Model -------------------------------
Cell Size = 6.750 CutOff Cell Size Factor = 0.500
Damping Cut-Off = 0.100 Dielectric = 1.000
Electrostatic Model = Delta/Gaussian Grid Cell/Cell Method = True
Inner Cut-Off = 8.000 List CutOff = 13.500
Minimum Cell Extent = 2 Minimum Cell Size = 3.000
Minimum Extent Factor = 1.500 Minimum Points = 500
Multipole Order = 0 Number of BP Atoms = 4
Outer Cut-Off = 12.000 RD Approximation = False
Sort Indices = False Spline Point Density = 50
Width 1 = 1.058 Width 2 = 1.058
------------------------------------ CutOff QC/MM Lennard-Jones Model ------------------------------------
Cell Size = 6.750 CutOff Cell Size Factor = 0.500
Damping Cut-Off = 0.500 Grid Cell/Cell Method = True
Inner Cut-Off = 8.000 List CutOff = 13.500
Minimum Cell Extent = 2 Minimum Cell Size = 3.000
Minimum Extent Factor = 1.500 Minimum Points = 500
Outer Cut-Off = 12.000 Sort Indices = False
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