GROMACS version: 2020.4
GROMACS modification: No
I built a membrane model in charmm-gui and have equilibrated it and have performed 100 ns MDS using parameters as described in the charmm-gui output files. Now I want to use the equilibrated membrane for other study but as I am adding water (TIP3P) using gmx solvate command the water in added in the box but it enters the spaces in between the membrane bilayer.
Also, while making the pbc box how do I define the box so that the water is only above and below the bilayer and not near and in the hydrophobic tail, which happened when I used “gmx editconf -f my_bilayer.pdb -o box.pdb -c -d 1.0 -bt cubic” tp over come this I defined the dimensions of the box manually using -box flag. So, let me know if its fine of there is a better way to do the same.