Installation Option B: Compiled Installation

Executable Compilation and Creation of a NGPB Image Optimized for your System:

Compile mcce with or without that of delphi, and the creation of a NGPB image optimized for your platform.

This option is necessary if you cannot run a simulation with an installation made with Option A: Automated Installation with scripts.

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

Clone MCCE4-Alpha to a desired place on your computer & cd into it:

git clone https://github.com/GunnerLab/MCCE4-Alpha.git; cd MCCE4-Alpha;

Add the clone’s bin paths to your .bashrc file then save it.

export PATH="clone_dir/MCCE4-Alpha/bin:$PATH"
export PATH="clone_dir/MCCE4-Alpha/MCCE_bin:$PATH"

Then apply the changes to your PATH variable by sourcing your .bashrc file, depending on your system.
Check a tool’s command correct path location (tools do not require compiling):
```
which p_info
```
The command should return ~/clone_dir/MCCE4-Alpha/MCCE_bin/p_info

2. Compiled components

MCCE4 contains C and C++ libraries that must be compiled prior to use. These consist of two executable files and a container image for the PBE solver, NGPB

mcce : Main simulation executable
delphi : Legacy PBE solver (support not guaranteed on all systems)
NextGenPB_MCCE4.sif : Container image for NGPB, the default MCCE4 PBE solver

We cannot guarantee that the DelPhi PBE solver executable (delphi) will run on your system. For this reason, NextGenPB (NGPB) is now the default PBE solver in MCCE4.

Currently, the MCCE4-Alpha Repository provides both the mcce and delphi compiled executables for Linux OS but the NGPB container requires sudo access to compile. Therefore, we also provide a Linux OS–> compiled NGPB container (NextGenPB_MCCE4_LinuxCompiled.sif) at the Dropbox link below.

👉 Download NextGenPB_MCCE4_LinuxCompiled.sif

Please place this in your MCCE4-Alpha/bin as NextGenPB_MCCE4.sif

Compile Executables and NGPB Container Image

If the provided executables and NGPB container do not work for your system, they must be compiled via the MakeFile. To proceed with compiling, please do the following:

Requires sudo access for the installation of the NGPB container (~15 min+).

Clean up previous versions, if any:

   make clean                  # remove bin/mcce and bin/delphi if present
   rm bin/NextGenPB_MCCE4.sif  # remove existing container image

Re-create the three objects: The screen output of this long compilation is extensive and not recoverable if not directed to a file, so there are two way to run the command: a. Without logging: make all

```
# individual compilation
make mcce
make delphi
make ngpb
```

b. Run make all command, with redirection to a log file:

     make all > make.log 2>&1

Or redirect logs for each target individually:

   make mcce   > make_mcce.log   2>&1
   make delphi > make_delphi.log 2>&1
   make ngpb   > make_ngpb.log   2>&1

To use the Openeye Zap solver, please see section PBE Solvers.

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