xTB

Using xTB for hybrid QC/MM calculations in pDynamo via the EasyHybrid interface is very straightforward. First, you need to install xTB and link it to pDynamo. There is a tutorial available on the pDynamo Wiki page that you can check out here.

Once xTB is properly installed, assigning a QC region to any system within EasyHybrid is simple. Just select the region of interest and use the "Set as QC atoms" option from the GL menu (accessed by right-clicking on the selection). This will open an auxiliary window for defining the QC region. In the "Method" field, choose the xTB option, and then a new auxiliary window will appear.

By default, EasyHybrid will use pDynamo’s scratch folder as the location for writing temporary files. However, it may be a good idea to choose a different directory if you plan to inspect the log files generated by xTB, and especially if you intend to run two different processes using xTB simultaneously!

Some useful tips:

1. Note that when you save a serialization file (.pkl), it contains all the parameters you’ve set, including the scratch folder and the path to the xTB executable. If this file is used on another computer, you will likely need to reassign the QC region, now using the correct paths for both the scratch folder and the xTB executable.

2. xTB can run in parallel by simply selecting the number of CPUs to use. However, for procedures like 2D scans and umbrella sampling, there is an opportunity for coarse-grained parallelization (i.e., running multiple independent processes simultaneously). In such cases, a simple calculation is required. Suppose you have 64 processors and plan to perform an umbrella sampling calculation with 32 windows running in parallel. In this scenario, it is more efficient to assign 2 CPUs per xTB process, ensuring that all 64 CPUs are utilized (32 x 2).