How to add polymers into the interface horizontally?

User discussions
1

Hi, I am new to GROMACS and am currently attempting to replicate a paper. I am trying to insert 4 number of the same polymer, i-PMA, into a CCl4-water interface. However, when using Packmol to add it, the molecule aligns vertically to the interface, whereas in the reference paper, it is positioned horizontally. To achieve this, I modeled a 7.8 x 7.8 x 15.6 nm^3 box containing a water-CCl4 interface, and minimized the energy. The polymer was obtained from the ATB and inserted into the water-CCl4 interface using Packmol. Unfortunately, the polymer remains vertical to the interface. How can I change its orientation?

Additionally, in the paper, the polymer is depicted in a curved shape, which differs from the downloaded polymer. Even after energy minimization, I did not obtain the desired pancake shape. How can I modify the shape of the molecule? I modeled the PDB format of the polymer containing 30 repeating units using Material Studio. I am attaching the Packmol input for my interface + polymer. Any assistance would be appreciated

water and carbon tetrachloride

tolerance 2.0
filetype pdb
output m486-i5cm-pma-box.pdb

adding 1400 moles of CCl4

structure M486.pdb
number 1400
inside box 0. 0. -78. 78. 78. 0.
end structure

adding 8340 moles of H2O

structure I5CM.pdb
number 8340
inside box 0. 0. 0. 78. 78. 78.
end structure

adding 4 moles of i-PMA

structure LBER.pdb
centerofmass
fixed 39. 39. 0. 0. 78. 0.
end structure

structure LBER.pdb
centerofmass
fixed 35. 39. 0. 0. 78. 0.
end structure

structure LBER.pdb
centerofmass
fixed 45. 39. 0. 0. 78. 0.
end structure

structure LBER.pdb
centerofmass
fixed 30. 39. 0. 0. 78. 0.
end structure

Please help

2

Two ways to address this:

  1. Use Packmol with “inside box” set for the 4 polymers such that the box dimension is where the CCl4-water interface lies. Keep the z-dimension size small so that the polymer is aligned in the xy plane.
  2. Make box of one solvent, lets say CCl4. Increase the box size in .gro file in z-direction by 1 nm (or more, depending on the polymer chain configuration). Either use gmx insert-molecules or manually copy the polymer coordinates in the CCl4 .gro file. Rotate the molecules to desired configuration using VMD. Save the coordinates. Again increase z-dimension of the box and then use gmx solvate to add water.
3

thank you @rpsingh . I will try both ways