Hi I am using editconf to try to add water layers on either side of my bilayer. I use the following command:
genbox -cp popc.gro -box 12.47820 12.35940 10.0 -o solvated.gro -cs spc216.gro -p topology.top However, because the center of the bilayer region is less dense, a lot of water molecules are created inside the bilayer. - How does one usually edit pdb files in gromacs, in terms of, for example, removing water molecules from the center of a bilayer ? Thank you -Maria -- Maria G. Technical University of Denmark Copenhagen
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