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6

I think the effect of larger cutoffs will not affect your simulation. Shorter cutoffs will be more problematic and can see artifacts than the larger cutoffs. Even if you have larger cutoffs, the interaction strength will be very very weak as you go outward and eventually die. This will just increase your computational cost (neighbour list calculation) and ...


4

One way could be as follow. Download software PACKMOL. Download the examples files (tar.gz or zip). Modify the file solvprotein-comment.inp: removing the info about the protein, and the ions and define the number of water molecules and the size of the droplet: # # Protein solvated by water and ions # # All atoms from diferent molecules will be at least 2....


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