Equilibration of polymer structure

Dear Sir,

I am working on polymer structure(Nafion). In my simulation box, polymer(Nafion) & water molecules are there. After defining forcefield & minimization steps properly I am trying to achieve equilibration of our structure. For this I am running NVT & NPT ensemble as per the literature. In literature the target density is 1.75g/cm3 but when I running the simulation my density cross this value & reach 2.7 g/cm3.
Can you please suggest where I am doing the mistake ?

This question is more about your project than a general discussion on the LAMMPS software. You should be discussing that with a colleague or an advisor. Beside, polymers are complicated systems, Nafion is a very complicated one (lot of chemical species) and you are extremely vague on the methodology you’re using. So there are a lot of places where things can go wrong and making guesses or suggestions with that few information is not very helpful.

Please consider the following points:

  • Which value from the literature are you referring to? Experimental value? A model value?
  • Was this value expected from your model?
  • Which model are you using? An all-atom or a coarse-grain model? From where does it come?
  • How did you make your initial configuration? How did you equilibrate it? For how long? What is your simulation procedure (including LAMMPS version and commands used)? These are important steps for polymer materials which can have very long equilibration/relaxation time.
  • Are you making the simulation at the same pressure and temperature than the reference? Is the value you are talking about a plateau value? How far are your expected thermodynamic parameters (P, T, \rho…) from your initial configuration?

Answering these questions might already clarify what you are doing for yourself. Your results and what to expect from your simulations are things to be discussed in the lab. That is where you can get tools and advices to be autonomous on doing MD simulation and how to lead your research project.

Thanks sir