Prof. Dr. Ademir Camargo

​The gQTEA program is a comprehensive molecular analysis application developed by the Theoretical and Structural Chemistry group from the State University of Goiás. It provides tools for analyzing molecular properties, generating computational inputs, and visualizing molecular structures. The main functionalities include remote host access, 3D molecular viewer, coordinate converter, bond length analysis, bond angle analysis, dihedral angle analysis, hydrogen bond analysis, cpmd inputs for wavefunction optimization, equilibration, and simulation using Car-Parrinello molecular dynamics and Born-Oppenheimer molecular dynamics, builds surface hopping inputs for excited-state dynamics, creates input files for collision simulations, selects specific frames from molecular dynamics trajectories, visualize cpmd energy outputs as plots, calculates the radial distribution function of molecular systems, determines the average time molecules spend in a specified region, computes time correlation functions for molecular properties, create a solvent box, makes a solvent box with a single solute, makes a box with mixture of solvent and solute, calculates power spectral density (PSD), calculates classical rate constante.Cada site tem uma história e seus visitantes querem saber a sua. Esse é um ótimo espaço para contar um pouco mais sobre você, o que a sua equipe faz e o que o seu site tem a oferecer. Clique duas vezes na caixa de texto para adicionar as informações que seus visitantes precisam saber.
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Molecular Viewer

The Molecule Visualizer is a graphical application designed to render and visualize molecular structures in 3D. It reads molecular data from XYZ format files and provides an interactive environment where users can manipulate the view to better understand the spatial arrangement of atoms and bonds within a molecule.
Upon launching the program, you'll see the main window with the following elements:
Select XYZ Format File: Text input field and a "Browse" button to select your molecule file. Set Bond Length: Text input field and a "Set bond length" button to define bond lengths. The default bond length is 1.5 Å.  A button to render and display the molecule in a new window. Opens a file dialog to select an XYZ format file; the file path will appear in the text input field next to "Select XYZ format file. Setting Bond Length. 
Note: Bonds involving hydrogen atoms use a fixed maximum distance of 1.2 Å. The molecule is rendered, and you can interact using mouse controls. Rotating the Molecule: Click and drag with the left mouse button to rotate the molecule around the X and Y axes. Use the mouse wheel (scroll up or down). Click and drag with the right mouse button to pan the view horizontally and vertically. Click and drag the edges or corners of the window to resize the window, and the visualization adjusts accordingly.
Sample XYZ File
5
Water Molecule
O    0.000000    0.000000    0.000000
H    0.757160    0.586260    0.000000
H   -0.757160    0.586260    0.000000
H    0.000000   -0.757160    0.586260
H    0.000000   -0.757160   -0.586260

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Customization and Features

Hydrogen atoms are displayed at half the size of other atoms for accurate representation.
Atom Colors:
H (Hydrogen): White
C (Carbon): Gray
O (Oxygen): Red
N (Nitrogen): Blue
Other Elements: Default gray color
Customization:
You can modify the atom_colors dictionary in the script to change colors or add new elements. Adjust the radii in the main_loop method if you wish to change atom sizes. Use the bond length specified in the "Set bond length" input field.
Hydrogen Bonds:
Fixed maximum distance of 1.2 Ångströms.
Customizing Bond Lengths:
To change the fixed distance for hydrogen bonds, modify the value in the calculate_bonds method: max_distance = 1.2  # Modify this value as needed

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Solvent Box Builder

The Solvent Box Builder is a graphical user interface (GUI) application designed to generate a three-dimensional solvent box for molecular simulations. It allows users to create a solvent box by placing solvent molecules in a defined lattice, with options to:
-    Randomly rotate solvent molecules.
-    Include a solute molecule at the center of the box.
-    Specify minimum distances between solvent molecules and the solute.
-    Use a mixture of two different solvents with specified compositions.
-    Calculate the density of the resulting solvent box.

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Input Fields:

-    Box Lattice Vectors: Text input for entering the lattice vectors a, b, and c.
-    Grid Spacing: Text input is used to enter the grid spacing.
-    Minimum Distance from Solute (Å): Text input for specifying the minimum distance between solvent molecules and the solute molecule.
-    Minimum Distance Between Solvents (Å): Text input for specifying the minimum distance between solvent molecules.
Switches:
-    Randomly Rotate Solvent Molecules: Option to apply random rotations to the solvent molecules.
-    Calculate Density: Option to calculate the density of the solvent box after generation.
Include Solute Molecule: Option to include a solute molecule at the center of the box.

Use Mixture of Solvents:

 
Option to use a mixture of two solvents.
Solute Selection:
-    Select Solute: Text input displaying the path to the selected solute molecule file.
-    Browse Button: Opens a file dialog to select a solute molecule file in XYZ format.
-    Solvent Selection:
-    Select Solvent A: Text input and browse button for the first solvent.
-    Select Solvent B: Text input and browse button for the second solvent (if using a mixture).
Composition Inputs (if using a mixture):
-    Composition of Solvent A (%): Text input for entering the percentage of solvent A.
-    Composition of Solvent B (%): Text input for entering the percentage of solvent B.
Output Display:
-    Output Text Area: Multi-line text area displaying logs, parameters, and results.
Control Buttons:
-    Read Params: Reads and validates the input parameters.
-    Build Box: Initiates the solvent box generation process.
-    Close: Closes the application.
Using the Solvent Box Builder
Step 1: Enter Lattice Vectors and Grid Spacing
-    Box Lattice Vectors:
-    Enter the lattice vectors a, b, and c separated by spaces.
-    Example: 20 20 20
Grid Spacing:
-    Enter the desired grid spacing as a positive float.
-    Example: 2.0
Step 2: Configure Minimum Distances
-    Minimum Distance from Solute (Å):
-    Enter the minimum distance between solvent molecules and the solute molecule.
-    Example: 2.5
-    Minimum Distance Between Solvents (Å):
-    Enter the minimum distance between solvent molecules.
-    Example: 1.5
Step 3: Include Solute Molecule (Optional)
-    Toggle the Include Solute Molecule switch on to include a solute molecule at the center of the box.
-    Click the Browse button next to Select Solute to select the solute molecule file in XYZ format.
The path to the selected file will appear in the Select Solute input field.
The content of the solute molecule file will be displayed in the Output Text Area.
Step 4: Select Solvent Molecules
-    Single Solvent:
-    Click the Browse button next to Select Solvent A to select your solvent molecule file in XYZ format.
The path to the selected file will appear in the Select Solvent A input field.
The content of the solvent molecule file will be displayed in the Output Text Area.
The mixture of Solvents:
Toggle the Use Mixture of Solvents switch on.
Click the Browse button next to Select Solvent A and Select Solvent B to select the solvent molecules.
The paths to the selected files will appear in the respective input fields.
The contents of both solvent molecule files will be displayed in the Output Text Area.
Step 5: Configure Solvent Mixture (Optional)
If using a mixture of solvents:
Enter the compositions of Solvent A and Solvent B in the respective input fields.
The compositions must be positive numbers that sum to 100%.
Example:
Composition of Solvent A (%): 40
Composition of Solvent B (%): 60
Step 6: Configure Additional Options
Randomly Rotate Solvent Molecules:
Toggle the switch on to apply random rotations to each solvent molecule placed in the box.
Toggle off to place solvent molecules without rotation.
Calculate Density:
Toggle the switch on to calculate and display the density of the generated solvent box.
Toggle off to skip density calculation.
Step 7: Build the Solvent Box
Click the Read Params button to validate and read the input parameters.
The parameters will be logged in the Output Text Area.
If there are errors, they will be displayed as dialog messages.
Click the Build Box button to generate the solvent box.
The application will perform the following steps:
Create a 3D grid based on the lattice vectors and grid spacing.
Center the solvent and solute molecules at the origin.
Fill the box with solvent molecules, applying random rotations if selected.
Ensure solvent molecules are not placed too close to the solute or to each other based on the specified minimum distances.
Use the specified compositions if using a mixture of solvents.
Save the solvent box data to an XYZ file.
Display the contents of the solvent box in the Output Text Area.
If Calculate Density is enabled, the density will be calculated and displayed.

Understanding the Output
The Output Text Area provides detailed information throughout the process:
Parameters: Displays the lattice vectors, grid spacing, minimum distances, and compositions entered.
Molecule Contents: Shows the content of the selected solvent and solute molecule files.
Solvent Box Contents: After building the box, displays the number of atoms and the coordinates of all atoms in the box.
Density Calculation: If enabled, displays the calculated density in grams per cubic centimeter (g/cm³).

Saving the Solvent Box
The solvent box data is automatically saved to an XYZ file named solvent_box.xyz in the same directory as the solvent molecule file.
The file includes:
The total number of atoms.
A comment line.
The list of atoms with their symbols and coordinates.

Troubleshooting
Invalid Lattice Vectors:
Ensure you enter exactly three numerical values separated by spaces in the Box Lattice Vectors field.
Example of valid input: 20 20 20
Invalid Grid Spacing:
Enter a positive numerical value in the Grid Spacing field.
Solvent Molecule File Issues:
Ensure the file is in the correct XYZ format.
The file should start with the number of atoms, followed by a comment line, and then the atom entries.
Compositions Do Not Sum to 100%:
When using a mixture of solvents, ensure the compositions of Solvent A and Solvent B add up to 100%.
Missing Solvent or Solute Files:
Ensure you have selected the required solvent and solute molecule files based on your configuration.
Minimum Distance Errors:
Enter positive numerical values for the minimum distances.
Ensure minimum distances are appropriate for your system dimensions.
Error Messages:
Error dialogs will appear if there are issues with the inputs or during processing.
Read the error messages carefully to identify and correct the problem.

Explique seus valores, seu compromisso com os clientes e como você se destaca no mercado. Adicione fotos ou vídeos para obter mais engajamento.

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