Simulation Analysis (post-simulation)

The post-simulation analysis is required to combine all the individual simulation files into the combined molecular trajectories or coordinate (DCD file), system Energies and State properties. The systems topology (PSF) file is not combined, but selected and copied to the combined data folder for easy use. Otherwise, without a data combining code, it would be nearly impossible to sort through all the individual GOMC and NAMD files and combine them all. The output from the combining file is dependent on the data input file (user_input_combine_data_NAMD_GOMC.json file) and the utilized ensemble. The simulation data combining file was designed for these hybrid simulations; however, it also works for the traditional GOMC-only or NAMD-only simulations, so the data is output in the same manner for easy comparison, if needed. The following sections show how the combining data files are output for the hybrid simulations. While the traditional NAMD-only and GOMC-only simulation combined data outputs contain their specific subset of the data.

Hybrid Simulation: NAMD Combined Energy Data

These combined NAMD outputs contain the Energy and State properties for the NAMD simulations. Each file also include the header/title, which is only printed once at the top of the files. A few NAMD output files are provided for easy utilization by the user. In these files the energy units are kcal/mol and the density is in g/cm^3.

  • NAMD_data_box_0.txt and NAMD_data_box_1.txt = The energy rows from each individual NAMD simulation are extracted directly from the NAMD log file and combined into a single file with the corrected time steps.

  • NAMD_data_density_box_0.txt and NAMD_data_density_box_1.txt = The energy rows from each individual NAMD simulation are extracted directly from the NAMD log file with the addition of the system density (g/cm^3) and combined into a single file with the corrected time steps.

    NOTE: The box 1 files are only generated for the GEMC ensemble when the user selects NAMD to run both box 0 and box 1.

Hybrid Simulation: GOMC Combined Energy Data

The combined GOMC outputs contain the Energy and State properties for the GOMC simulations, which are listed in two (2) separate lines (i.e., for example, ENER_0 and STAT_0 for box 0 or ENER_1 and STAT_1 for box 1). Each file also include the header/title, which is only printed once at the top of the files. There are several GOMC output files provided so the user has some options.

NOTE: Box 1 is listed as an output in the below examples, is only printed for the GEMC ensemble since box 1 serves no meaning or is not present in the GCMC, NPT, and NVT ensembles.

  • GOMC_data_box_0.txt and GOMC_data_box_1.txt = The Energy and Stat data are output for each simulation box as they are extracted exactly as is from the GOMC log file (energy units are in K and the density units are in kg/m^3).

  • GOMC_Energies_Stat_box_0.txt and GOMC_Energies_Stat_box_1.txt = The Energy and Stat data are extracted for each simulation box from the GOMC log file, and they are appended together as a single line with the ENER_X and STAT_X labels removed. The energy units are in K, and the density units are in kg/m^3.

  • GOMC_Energies_Stat_kcal_per_mol_box_0.txt and GOMC_Energies_Stat_kcal_per_mol_box_1.txt = The Energy and Stat data are extracted for each simulation box from the GOMC log file, and they are appended together as a single line with the ENER_X and STAT_X labels removed. The energy units are in kcal/mol, and the density units are in g/cm^3.

Hybrid Simulation: GOMC and NAMD Coordinates/Topology (DCD/PSF)

The GOMC and NAMD coordinate (DCD) and topology (PSF) files can be output using the combining data python code, per the users input. However, for the GCMC and GEMC ensembles, only the PSF and DCD files are output for the GOMC simulation since a NAMD simulation is not currently capable of handling a changing number of atoms. For example, both the combined NAMD and GOMC PSF and DCD files can be output for the NPT and NVT ensembles, but only the GOMC PSF and DCD files can be output for the GCMC and GEMC ensembles. The output will be as follows:

NOTE: The box 1 PSF and DCD files will only be output for the GOMC simulation using the GEMC ensemble.

  • Output_data_merged.psf = The topology (PSF) file is used with the combined coordinate (DCD) files to identify the bonds, angles, dihedrals, impropers, and other atoms naming and properties. If this is a GCMC or GEMC ensemble, the topology (PSF) file will contain atoms from both box 0 and box 1.

  • combined_box_0_GOMC_dcd_files.dcd and combined_box_1_GOMC_dcd_files.dcd = The combined coordinate (DCD) files from all the individual GOMC simulations, or at the selected frequency set by the user input file for combining the data.

  • combined_box_0_NAMD_dcd_files.dcd = The combined coordinate (DCD) files from all the individual NAMD simulations, or at the selected frequency set by the user input file for combining the data. This combined NAMD coordinate (DCD) is only output for the NPT and NVT ensembles.

Hybrid GCMC Simulation: GOMC Histogram and Distribution Data

The histogram and distribution data are combined and output only for a GOMC simulation using the GCMC ensemble. Please refer to the GOMC Manual for more information on the histogram and distribution data. The files are listed as follows.

  • GOMC_hist_data_box_0.txt = The combined histogram data for the individual simulations.

  • GOMC_dist_data_box_0_res_or_mol_no_XXX.txt = The combined distribution data for each molecule type in the individual simulations. There will be one (1) combined distribution data file generated for each molecule type in the simulation, and they will replace the no_XXX in the file name with no_1, no_2, etc.

Hybrid, GOMC-only, or NAMD-only Combining Data Input Variables

These variables are used when running combining the data code for the hybrid MD/MC simulations. However, they can also be used for the traditional GOMC-only or NAMD-only simulations, allowing the user to easily compare between the simulations. The selected variables will determine how the data combining code functions and thus how the data is output. Therefore, the user should ensure that the selected variables are in-line with the simulation which was conducted, or the output data will be lacking or fail to be generated.

The variables below are contained in the “user_input_combine_data_NAMD_GOMC.json” file, which is the in the “NAMD_GOMC/analysis_combine_data” directory. When the variables are not used for the particular simulation type (‘Hybrid’, ‘GOMC-only’, ‘NAMD-only’), the inputs still need to be supplied. However, the only requirement for the unused variables is that a string, boolean, or allowable types and values its requests is provided. The combining file will start and run correctly, provided all the required variables are correct.

simulation_typestring (only ‘GEMC’, ‘GCMC’, ‘NPT’, ‘NVT’)

The simulation type or ensemble to use. Note: only GEMC-NVT available currently (‘GEMC’ = GEMC-NVT). This is required for all combining types (‘Hybrid’, ‘GOMC-only’, ‘NAMD-only’).

only_use_box_0_for_namd_for_gemcbool (true or false)

This chooses if you run both simulation boxes in NAMD when running the GEMC ensemble, or just box 0. true = NAMD run only box 0 for GEMC false = NAMD run box 0 and 1 for GEMC This input is used when combining the ‘Hybrid’ data. This is required when combining the ‘GOMC-only’, or ‘NAMD-only’ data, but is not used.

simulation_engine_optionsstring (‘Hybrid’, ‘GOMC-only’, ‘NAMD-only’)

The type of simulation you are combining. ‘Hybrid’ is the hybrid NAMD_GOMC simulations. ‘GOMC-only’ is stand-alone GOMC simulation. ‘NAMD-only’ is stand-alone NAMD simulation. This is required for all combining types (‘Hybrid’, ‘GOMC-only’, ‘NAMD-only’).

gomc_or_namd_only_log_filenamestring

The relative path and file name of the log file for the GOMC-only or NAMD-only simulation, which is used to create the same file format as the hybrid simulation combining files. This input is used when combining the ‘GOMC-only’, or ‘NAMD-only’ data. This is required when combining the ‘Hybrid’ data, but is not used.

combine_namd_dcd_filebool (true or false)

This chooses if you want combine all the NAMD dcd files into one file for all the Hybrid NAMD simulations. This option is only possible for “NVT” and “NPT” ensembles. true = combine all the NAMD dcd files false = do not combine all the NAMD dcd files This input is used when combining the ‘Hybrid’ data. This is required when combining the ‘GOMC-only’, or ‘NAMD-only’ data, but is not used.

combine_gomc_dcd_filebool (true or false)

This chooses if you want combine all the GOMC dcd files into one file for all the Hybrid GOMC simulations. This option available for all the ensembles. true = combine all the GOMC dcd files false = do not combine all the GOMC dcd files This input is used when combining the ‘Hybrid’ data. This is required when combining the ‘GOMC-only’, or ‘NAMD-only’ data, but is not used.

get_initial_gomc_dcdbool (true or false)

true = This chooses whether to add the initial GOMC dcd trajectory to the combined GOMC dcd files, based on the existing ‘GOMC’ directory (i.e., the 1st GOMC dcd trajectory in the 1st GOMC individual simulation which are currently in ‘GOMC’ directory).

false = It will not add the initial dcd file from the first GOMC folder to the combined dcd file. Example: It may be useful to not include the first folders initial dcd trajectory when users are conducting the piecemeal simulations, deleting the individual simulation folders as they go. In this example, the user would need to combine the separate dcd files that are created this way outside of this program.

Note: NAMD does not allow this option; however, when NAMD dcd file are able to be combined (NPT and NVT ensembles). For NAMD, the simulations starting PDB file can be loaded into the trajectory in VMD or other software, which will allow user to access all the data.

rel_path_to_combine_binary_catdcdstring

The relative path and file name to the catdcd, which are provided from the Theoretical and Compuational Biopyysisc group (VMD/NAMD development team) (https://www.ks.uiuc.edu/Development/MDTools/catdcd/). This tool is used to combine the dcd files for the hybrid simulations. Note: there are various catdcd files for different CPUs and operating systems, so please select the proper only for your system. This input is used when combining the ‘Hybrid’ data. This is required when combining the ‘GOMC-only’, or ‘NAMD-only’ data, but is not used.

rel_path_to_NAMD_and_GOMC_foldersstring

The relative path to the main NAMD and GOMC folders which contain all the individual simulations. This is also where the run_NAMD_GOMC.py file is located, as it build the NAMD and GOMC folders in the same directory. This input is used when combining the ‘Hybrid’ data. This is required when combining the ‘GOMC-only’, or ‘NAMD-only’ data, but is not used.