Fixed atoms
In pDynamo3 simulations, as well as in EasyHybrid, it is possible to freeze or fix groups of atoms during the process. To achieve this, follow these steps:
Select the group of atoms you wish to freeze or fix.
Access the main menu and locate the "Selections" item.
In the "Selections" menu, choose the option to assign the selected atoms as "fixed."
Alternatively, you can access the GL area selection menu by right-clicking with the mouse button (mouse button 3).
In the GL area selection menu, select the "Set as fixed atoms" option.
By performing these steps, you can designate the selected atoms as fixed, ensuring that their positions remain unchanged during the simulation or other related processes. When selected atoms are assigned as fixed in EasyHybrid, they are represented by default in gray color. This visual representation helps differentiate the fixed atoms from the rest of the atoms in the system. By default, the gray color is used to indicate that these atoms are fixed and their positions will remain unchanged during the simulation or other processes (Figure 1).
Select the group of atoms you wish to freeze or fix.
Access the GL area selection menu by right-clicking with the mouse button.
By default, the gray color is used to indicate that these atoms are fixed.
Figure 1: Fixed assignment for selected atoms. By default, EasyHybrid represents fixed atoms in gray.
The assignments of atoms in the fixed condition in EasyHybrid are additive. This means that if the selection process is performed multiple times, the number of fixed atoms will be the sum of the selected atoms in each process. By repeatedly selecting additional atoms, you can gradually add them to the group of fixed atoms.
To make a group of atoms free (i.e., unfixed), a similar process is followed. The user selects the atoms of interest and then accesses the "Selections" item in the main menu. From there, the user can choose the "Set as Free Atoms" option. Alternatively, the same option can be accessed from the GL area selection menu. This process allows you to remove the fixed assignment from the selected atoms, making them free to move and interact during simulations or other processes.