Dears,
I am a beginner in simulations.
I am trying to put some surfactants in a water/oil interface, fixing * and orienting the molecules at the interface with the hydrophilic head directed towards the water and the hydrophobic towards the oil.
Using Packmol I was able to create the box with water/surfactant / oil/surfactant/water, but I could not create a space between the water and the oil to place the surfactants and I could not even fix the molecules.
* I need to fix them so they do not interact with each other at the beginning of the simulation.
** I need this empty space to vary the number of molecules in the interface and then decrease the size of the box using NPT.
In the Packmol user guide, I saw in the examples that you have how to fix only one molecule:
"structure molecule.pdb
number 1
center
fixed 0. 0. 0. 0. 0. 0.
end structure "
In this example, one molecule will be fixed with its center the origin and no rotation, but I do not know if I would have to fix several molecules at the same time.
I really appreciate it if you may help me.
Kind regards.
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