I am doing a simulation with polymer(PIM-1) having water on both side of it ( picture attached). To insert the water molecules inside the polymer membranes , I am giving a 1 bar pressure on both side of the graphene wall . Using the LAMMPS add force command , I have applied a force of 0.0000377 (kcal/mol)/Angstrom ( as I am using real unit) to generate a pressure of 1 bar on each side with the graphene membrane. However, the polymer started to squeeze when the pressure was applied to it from both sides with water molecules and the water molecules couldn’t get inside to it.
Is there any command in LAMMPS that I can use, so that the polymer might not squeeze this much & the water molecules can get inside to it?
For your reference, I am using lammps version 2 Aug 2023.
Its a side note to your question, but are you sure that the pressure is only 1 bar? The water looks ultra compressed which would only occur at much higher pressure.
There is no “make the atoms behave the way I want them to” command in LAMMPS.
Atoms go where the forces tell them to go. You are defining the forces through the force field parameters and the magnitude of your external force. If the trajectory is not what you expect, either the forces are not representative of what you want to model or your expectations.
Based on the comment of @simongravelle: have you checked the pressure components of your system in the periodic directions of your system? Are they at 1 bar or higher?
Has your system equilibrated? I find that whenever I’ve tried applying force to a carbon sheet to mimic pressure, the carbon sheets’ separation fluctuates wildly – I attribute that to carbon being “too light”. A poorly compressible system will throw out big pressure waves en route to equilibration, especially if started from an improperly small or large initial volume, and a piston with too little density like carbon will fluctuate in response, often too much for a typical MD box to handle.
(Or maybe I’ve just been doing it wrong all this while?)
In your position I would start simple: run a “constant volume” simulation by completely not integrating the wall particles; track the density profile of the water across the system using some fix ave/chunk; if the water density right in the middle of the polymer-free zone is correct (1 g/cc) and the water density permeating into the polymer is stable over time, then you at least have a baseline for attempting barostatted simulations. You can even estimate the pressure on the walls using compute group/group between (for example) the left wall and all non-wall atoms; the average total wall force will be the effective pressure, times cross-sectional area.
Alternatively, use fix langevin with a very high friction coefficient to damp the graphene walls’ vibrations, instead of whatever thermostat you currently use. How high? High enough to get the “correct answer”. What’s the correct answer? I wouldn’t know, but the constant volume simulations would give you at least some clue.
