Exercise Four: Test Different Meshes

In this exercise, we will explore how to modify the mesh resolution in NextGenPB and observe its impact on the calculated electrostatic potential.

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Step 1 – Prepare the Inputs

Navigate to the working directory for this exercise:

cd ~/ngpb_tutorial/ex4

Copy the necessary input files:

cp ../NextGenPB/data/1CCM.pdb .
cp ../NextGenPB/data/charge.crg .
cp ../NextGenPB/data/radius.siz .

Create Parameter Files

We will prepare multiple parameter files to test different mesh resolutions by varying the scale, the perfil, and by applying random displacement of the mesh center.

A full description of mesh options is available in the Guide

Fine Mesh (fine_mesh.prm)

Create a file named fine_mesh.prm in the current directory with the following content:

[input]
filetype = pdb
filename = 1CCM.pdb
radius_file = radius.siz
charge_file = charge.crg
write_pqr = 1
name_pqr = 1CCM_out.pqr
[../]

[mesh]
mesh_shape = 0
perfil1 = 0.95
perfil2 = 0.2
scale   = 4.0
[../]


[model]
bc_type = 1                                
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

map_type      = vtu   # Output format: 'vtu' (for ParaView, vtk binary), 'oct' (Octbin internal format)
potential_map = 1     # 1 = write full potential map to file
[../]

This will produce a mesh with a grid scale in the region of perfil1 equal to 0.25 Å.

Random center (rand_center.prm)

Create a file named rand_center.prm in the current directory with the following content:

[input]
filetype = pdb
filename = 1CCM.pdb
radius_file = radius.siz
charge_file = charge.crg
write_pqr = 1
name_pqr = 1CCM_out.pqr
[../]

[mesh]
mesh_shape = 0
perfil1 = 0.95
perfil2 = 0.2
scale   = 2.0
rand_center = 1 
[../]

[model]
bc_type = 1                                
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

map_type      = vtu   # Output format: 'vtu' (for ParaView, vtk binary), 'oct' (Octbin internal format)
potential_map = 1     # 1 = write full potential map to file
[../]

This will randomly shift the mesh center within an interval of one grid scale.

Focusing (focus.prm)

Create a file named focus.prm in the current directory with the following content:

[input]
filetype = pdb
filename = 1CCM.pdb
radius_file = radius.siz
charge_file = charge.crg
write_pqr = 1
name_pqr = 1CCM_out.pqr
[../]

[mesh]
mesh_shape = 3
perfil1 = 0.9
perfil2 = 0.2
scale   = 2.0

cx_foc  = 1       # X-center of focusing region
cy_foc  = 10       # Y-center of focusing region
cz_foc  = 5       # Z-center of focusing region
n_grid  = 50      # Number of 1/scale-width intervals in focused zone
[../]

[model]
bc_type = 1                                
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

map_type      = vtu   # Output format: 'vtu' (for ParaView, vtk binary), 'oct' (Octbin internal format)
potential_map = 1     # 1 = write full potential map to file
[../]

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Step 2 – Run the Solver

Now launch the simulation using Apptainer:

Refined grid

apptainer exec --pwd /App --bind .:/App ../NextGenPB.sif mpirun -np 4 ngpb --prmfile fine_mesh.prm

Random center

apptainer exec --pwd /App --bind .:/App ../NextGenPB.sif mpirun -np 4 ngpb --prmfile rand_center.prm

Focusing

apptainer exec --pwd /App --bind .:/App ../NextGenPB.sif mpirun -np 4 ngpb --prmfile focus.prm

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➡️ For more information, see the Guide.