Installation Option A: Automated Installation

Quick Installation with Scripts

Keep the provided mcce and delphi (alternate PBE solver) executables compiled for Linux OS;
Use the semi-automated setup using provided script that download a generic NGPB image.

1. Clone the repository to a desired place on your computer (referred to as “clone_dir”):

Git clone MCCE4-Alpha to a desired place on your computer (copy & pasted this command and press Enter):
```
git clone https://github.com/GunnerLab/MCCE4-Alpha.git; cd MCCE4-Alpha;
```

2. Run the quick installation script

Script ./MCCE_bin/quick_install.sh automates the conda environment creation, export the clone references to the PATH variable in your .bashrc file, and download a generic NGPB image. Run:

bash ./MCCE_bin/quick_install.sh

The quick installation is completed by following the instructions displayed on the screen.

3. Installation Test 1: Is the generic image of NGPB running?

We test that NextGenPB is correctly set up by running a basic electrostatic potential calculation using a real protein input.

Prepare the Inputs:

Enter the test directory in your MCCE4-Alpha clone:

CLONE=$(dirname $(dirname "$(python3 -c "import os, sys; print(os.path.realpath(sys.argv[1]))" "$(which mcce)")")); echo "CLONE: $CLONE"; cd $CLONE/ngpb_test

Inside the ngpb_test/ , you will find a options.prm file and a .pqr file of a small protein. Example options.prm file:

[input]
filetype = pqr
filename = 1CCM.pqr
[../]
   
[mesh]
mesh_shape = 0
perfil1    = 0.95
perfil2    = 0.2
scale      = 2.0
[../]
   
[model]
bc_type                       = 1          # Boundary condition type
molecular_dielectric_constant = 2          # Dielectric constant inside the molecule
solvent_dielectric_constant   = 80         # Dielectric constant of the solvent (e.g., water)
ionic_strength                = 0.145      # Ionic strength (mol/L)
T                             = 298.15     # Temperature in Kelvin
calc_energy                   = 2
calc_coulombic                = 1
[../]

Run NGPB:

Run the simulation using Apptainer:
```
apptainer exec --pwd /App --bind .:/App ../bin/NextGenPB_MCCE4.sif ngpb --prmfile options.prm
```
This command runs NextGenPB inside the Apptainer container, binding your current directory (.) to /App` within the container.

Output and Results: At the end of the execution, you will see a log similar to this:

================ [ Electrostatic Energy ] =================
  Net charge [e]:                                 7.327471962526033e-15
  Flux charge [e]:                                -4.859124220152702e-11
  Polarization energy [kT]:                       -384.6169807703798
  Direct ionic energy [kT]:                       -0.2516508616874018
  Coulombic energy [kT]:                          -10097.24155852403
  Sum of electrostatic energy contributions [kT]: -10482.11019015609
===========================================================
compute energy
Elapsed time : 141.198ms
...

These outputs confirm that NextGenPB is functioning correctly and that your configuration is valid.

The timing report and energy terms provide a quick verification of the solver’s performance.

TODO: Indicate what to do if NGPB does not run: post issue or do the compiled installation?

4. Installation Test 2

Activate a dedicated environment. Choose either Option 1 or 2 below to create the environment:

Option 1: To use the conda environment created by the quick install script:
```
   conda activate mc4
```

Option 2: Alternate way with pyenv (conda is not abolutely necessary):

   pyenv virtualenv 3.10 mc4
   pyenv activate mc4
   pip install -r ../requirements.txt

Check that a tool is functional; Its usage message should display:
```
    p_info
    p_info -h
```

✅ Great! You have successfully installed and ready to run simulations now with MCCE4-Alpha!

➡️ Now, please proceed to the MCCE4-Tools Installation page to install our companion repository, MCCE4-Tools, which provides post-simulation analysis utilities -> no compilation of exectables required, just a simple repository clone and PATH setup.

To access the MCCE4-Tools Github codebase repository please click here! 🧰 MCCE4-Tools GitHub