GROMACS modification: Yes/No
I am simulating a chitosan film in contact with water molecules and I want to delete all water molecules solvated inside the film, I use command:
gmx select -s filmwithwater.gro -n index.ndx -on waterunwanted.ndx -select ’ “close to name Other” group 6 and within 0.6 of group 1’
In which Other is the film and group 6 is SOL, group 1 is Other.
My problem is using this method, I got an index file of all the atoms that within 0.6nm of the chains of the film, but not water molecules, there’re some water molecules are broken and left H or O atoms along in the box, as you ca see in the screen shot.
Could anyone help me with my issue? Does anyone know how can I select all the water molecules near or inside the film, as the edge of the film is not flat.
I already tried to insert two waterboxs on both sides of the film but due to the ununiform contact surface with water , the film tends to in contact with water on one side and be dragged to that side first during npt equilibrium, in this way I can’t properly observe the water absorbance(swelling behavior of the film). Many thanks in advance.