Import a new system

pDynamo is a highly versatile library, and fortunately, it supports various file formats and force fields. Consequently, EasyHybrid is also capable of importing this data. To import a new system, you can access the main menu by clicking on "File" > "New", or simply press the first button on the toolbar labeled "Import a new system"."

Figure 1: Accessibility options for importing a new system within the EasyHybrid interface.

The window for importing a new system (Figure 2) requires the following data:

• Name: This is the name that the user will give to identify the system within the interface.

• Tag: It is a sequence of characters that will be added to the names of processes and objects generated. This helps in organizing and storing trajectory and log data more efficiently.

• System Type: This refers to the type of system/force field that the user wants to work with. pDynamo is compatible with the main force fields used in molecular simulations of biological interest.

1. AMBER: It requires externally generated topology and coordinate files (referred to as top and crd files) for amber systems. These files are usually generated using ambertools.

2. CHARMM: It requires externally generated parameter files (prm), topology files (psf), and coordinate files (pdb, chm, xyz, etc.) for systems that use force fields from the CHARMM family. In some cases, multiple parameter files may be required.

3. OPLS: It requires files containing topological and coordinate information (pdb or mol2 format) as well as force field parameters. pDynamo stores this information in a folder that contains the parameter files. The force field data can be accessed at: ../pDynamo3/parameters/forceFields/opls.

4. DYFF: It is very similar to OPLS, but it links the system to the universal force field. You need a file containing coordinates and topological information (mol2 format is recommended) as well as a folder containing the force field parameters. If a mol2 file is used as input, the partial charges present in the file will be assigned to the respective atoms and considered in the calculations of non bonded interactions.

5. pDynamo files: It requires system files that are generated in pDynamo and exported in their respective serialization formats, typically pkl files. In this case, there is no need to specify whether or not the system is associated with a force field.

6. Other: Any other coordinate files that are compatible with pDynamo can be used. However, in this case, the loaded system will not be associated with a force field, and only quantum chemistry (QC) calculations will be allowed.

• Color: It is the reference color that will be used to highlight the system within the interface. When a new set of coordinates is generated in the form of a viewable object for the system in question, the carbon atoms will be associated with the chosen reference color for the system by default.

Figure 2: Window to import a new system in EasyHydrid. In this example a system using files generated for the AMBER force field are being used.

If everything has worked as expected, you should now see a wireframe representation in your GL area (Figure 3). Please keep in mind that the carbon atoms will be colored based on the reference color you have chosen.

Figure 3: Amber system loaded on EasyHybrid.