Basic Command Syntax

The most common way to run NextGenPB is through the mpirun command, which enables parallel execution using MPI (Message Passing Interface).
Even though the solver is designed for parallelism, you can use it with any number of processors, starting from 1:

mpirun -np <number_of_processors> ngpb --prmfile options.prm

Let’s break this down:

  • mpirun is the standard MPI launcher command.
  • -np <number_of_processors> tells MPI how many parallel processes (or “ranks”) to run. This number must be greater than or equal to 1.
  • ngpb is the executable name for the NextGenPB solver.
  • --prmfile options.prm is a required argument that specifies the simulation parameters.

If your simulation also involves a specific molecular structure, you can provide a .pqr file that contains atomic coordinates and charges:

mpirun -np <number_of_processors> ngpb --prmfile options.prm --pqrfile molecule.pqr

Details about the structure and purpose of .prm, .pqr, and .pdb files are provided in the Input Files guide.