Single points and energy refinement

Single points are simply energy calculations for a given set of coordinates. In EasyHybrid, single point calculations represent a fundamental functionality for the accurate evaluation of the energy of a molecular system at a fixed geometry. These calculations are particularly useful at various stages of a simulation protocol, such as comparing the energies of different conformations, constructing potential energy surfaces, or serving as a basis for subsequent analyses, such as thermodynamic corrections or reaction coordinate projections. In the context of EasyHybrid, this operation can be performed using pure quantum chemical methods (including ab initio and semiempirical approaches), molecular mechanics with force fields such as AMBER, CHARMM, or OPLS, or within hybrid QC/MM schemes, combining the electronic detail of an active region with the computational efficiency of a classical environment.

The Single point energy calculations can also be performed by accessing:

Main Menu > Simulate > Single Point Energy

An overview of the window for Single Point Energy can be seen in Figure 1.

In EasyHybrid, the reference system is determined by the active radiobutton in the treeview of the main window (note that each system is associated with a reference color).

• Coordinates: Refers to the visualizable object; the combobox only displays objects associated with the selected system.

• Frames: Indicates the reference frame; -1 refers to the last frame.

• Logfile: Name of the log file that will be generated.

• Working Folder: The working directory where output files will be generated. Temporary files created by programs such as ORCA, DFTB+, and xTB are saved in folders assigned when these programs are configured for a QC region—typically the "scratch" folder defined by pDynamo.

Energy refinement calculations are essentially an application of single point energy calculations to an entire trajectory (including two-dimensional scans). In this case, the tool also allows for parallel execution by splitting the task into independent processes. Once again, the reference system is determined by the active radiobutton in the treeview of the main window.

The Energy Refinement can be accessed via:

Main Menu > Analysis > Energy Refinement

An overview of the Energy Refinement window is shown in Figure 2.

Input Type: Refers to the type of input trajectory. Currently, only the pDynamo format (.ptGeo) is supported, for both one-dimensional and two-dimensional trajectories.

File / Folder: Specifies the folder containing the trajectory.

Number of CPUs: Defines the number of CPUs to be used. Each energy calculation for a trajectory frame is treated as an independent process. If you are using ORCA, DFTB+, or xTB in a multiprocessing mode, ensure that the total number of processes does not exceed the number of available CPU cores.

Set MM Charges to Zero: Ignores MM charges during the energy refinement.

A reaction coordinate must be assigned to associate energy values with specific configurations. This choice is arbitrary and does not need to match the coordinate used in the preliminary sampling scans.