Running the Simulation

The hybrid NAMD/GOMC simulation can be conducted once the “user_input_NAMD_GOMC.json” file is properly filled out to the user’s specifications, including generating or obtaining the proper PSF, PDB, and force field (.inp or .par files) and specifying their proper paths.

Example # 1: GEMC Ensemble

Use a terminal window and move to the directory which contains the run_NAMD_GOMC.py file. Then run hybrid NAMD/GOMC simulations with the NAMD simulations for box 0 and box 1 executed in parallel (assuming both boxes are being simulated in NAMD per the “user_input_NAMD_GOMC.json” file).

cd "directory_containing_run_NAMD_GOMC.py"

python run_NAMD_GOMC.py -f user_input_NAMD_GOMC.json -namd_sims_order parallel

Example # 2: GCMC Ensemble

Use a terminal window and move to the directory which contains the run_NAMD_GOMC.py file. Then run hybrid NAMD/GOMC simulations.

NOTE: The NAMD simulations default too in series, but it does not matter since the GCMC simulations box 1 is solely used as a reservoir without the need to evaluate the box’s dynamics.

cd "directory_containing_run_NAMD_GOMC.py"

python run_NAMD_GOMC.py -f user_input_NAMD_GOMC.json

Flags for Running the Hybrid Simulation

The flags for running the run_NAMD_GOMC.py file user_input_variables_NAMD_GOMC.json file, or whatever the user names it.

-f or –filejson file

Defines the variable inputs file used for the hybrid NAMD/GOMC simulation script. This file, the “user_input_variables_NAMD_GOMC.json” file, is required to run the hybrid simulation.

-namd_sims_order or –namd_simulation_orderdefault=’series’, (options: ‘series’ or ‘parallel’)

This sets the NAMD simulation to be run in series or parallel. The data is entered only as series or parallel (default = series). This is only relevant for the GEMC ensemble when utilizing two (2) NAMD simulation boxes (i.e., only_use_box_0_for_namd_for_gemc = False –> both box 0 and box 1). The GCMC, NVT, NPT, or the GEMC ensembles when using only one (1) NAMD simulation box (i.e., only_use_box_0_for_namd_for_gemc = True –> only box 0) are always run in series, since there is nothing to run in parallel. Note: This feature was added so the user can minimize the load on the GPU by running both NAMD simulations in parallel.