Running the Combining Data Code

The simulation data combining code is run via Python and combines all the required data into a few files for an easy simulation analysis. The data combining code is located in the “analysis_combine_data” file directory in the main directory (i.e., “NAMD_GOMC/analysis_combine_data”). Before running the data combining code, the user will need to fill out the proper input variables in the “user_input_combine_data_NAMD_GOMC.json” file, located in the same directory since this file determines how the data combining code is processed. The “user_input_combine_data_NAMD_GOMC.json” file name can be changed to whatever the user desires.

This code is designed to combine the hybrid simulation data into a central location. However, it can also be used to generate the same file types for a traditional NAMD-only or GOMC-only simulation, so the user can easily compare between the simulations.

Executing the Combine Data Code

The combine data code is run from its file directory via a terminal window.

NOTE: If the “user_input_combine_data_NAMD_GOMC.json” file variables are not set properly for the type of simulation that was conducted, the output will not work, or data will be missing.

cd "directory_containing_run_NAMD_GOMC.py"

python run_NAMD_GOMC.py -f user_input_combine_data_NAMD_GOMC.json -w combined_data -o False

Flags for Combining Data Code

• -f or –file flagjson file

  Defines the json file to use for variable inputs to the hybrid NAMD/GOMC, NAMD-only, or GOMC-only combining code.

• -w or –write_folder_name flagstr

  Defines the folder name which is created and contains the all the combined data files.

• -o or –overwrite flag(True, true, T, t, False, false, F, or f), default = False

  Determines whether to overwrite an exiting combined data folder and data, if they exist.