I am trying to build a realistic Nafion-based PEM system (polymer + water + hydronium) using Amorphous Cell + MD in Materials Studio.

Polymer details:

• Fluorinated backbone (–CF₂–CF–)
• Side chains with –SO₃H groups
• Water and H₃O⁺ are added separately during amorphous cell construction

• Approx. composition: C109 H12 O60 F208 S12

  Amorphous packing Gives:

• Poor distribution
• Most Atoms outside the box

• Unstable structure after MD Run

  After MD run the atoms are moving out of the box.

  Also Is there any other approach for this work?