I want to simulate polyelectrolyte of PPO . I inserted counterions into the simulation box and changed their position near the protonated group with position.dat file. but after minimization and NVT, the ion gotaway from protonated gruop (N+). why this happened?
Thank you in advance
The ion is not bonded to the protonated N+ in the PPO you are simulating. It is just interacting as any particle would via LJ/coulombic interactions. Ion-ion interactions come and go/break and re-form throughout a simulation
Theoretically, if you want to keep it in place, you could put a position restraint between the (presumably negative) ion and your N+, but I don't really know how valid that would be. Does the ion *need* to be interacting with the protonated group?
John H Dupuis
Dear John
Thank you very much for your reply. You are right. Actually ion and protonated group interact but not as a bonded interaction. I had a problem in concept but I figured it out. Actually it was right to getaway after NVT and NPT. I used gmx distance to see the distance frequencies. Ion-ion interactions break and reform again.
Thank you again for your kind response.
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