Dear all,
I want to calculate the density of water in cnt at 300 K and 1 atm (cnt connected to the two reservoirs of water). then as in the papers said i want to simulate a single cnt and filled it with that density obtained in the previous step. I'm using lammps. how could i calculate the density of water in cnt?
after that how i simulate the new cnt with that density? which program or software should i use?
Any idea and example of such simulation will be appreciated.
Best
There are various ways of doing this.
You can simulate a cnt in a bigger simulation box filled with water. The cnt will then automatically fill itself and by applying a barostat you ensure that you remain at atmospheric pressure as part of your water molecules fill the tube. You can then just write a data file with the tube and everything in it. However, since you describe that you need a tube connected to reservoirs, you can just fill the reservoirs with water and it will flow into the tube easily. You then just apply a barostat to the direction of the tube.
Furthermore, VMD and PackMol are able to solvate systems, or certain parts of systems. Keep in mind that the solvation (at least in PackMol, I'm not sure about VMD) is based purely on geometrical considerations assuming a bulk fluid. So the density might be slightly off, which can have large consequences for pressure, or other quantities.
Finally, you could use Grand Canonical Monte Carlo to add the right amount of water. For example Lammps can do this. However, this tends to be a slow process that cannot be parallelized.
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