[gmx-users] solvate using genbox results in water in the center of the bilayer. How to edit pdb file contents in gromacs ?

maria goranovic mariagoranovic at gmail.com
Sun Oct 21 12:27:36 CEST 2007


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 G.
Technical University of Denmark
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