[gmx-users] how to introduce vacuum??

Pedro Alexandre Lapido Loureiro paloureiro at biof.ufrj.br
Wed Aug 6 01:06:01 CEST 2003

> hi,
> 1: i have one water box with a protein & some other molecules. the height (
> 'c' in the dimensions of the system) of the box is 60 angstroms. Now I have
> to introduce vacuum in a section of the box ( say from height of 45 AU to 
> 55 AU)  how do i do that??
If you want vacuum "above" the water layer then it`s easy: just enlarge the box
with editconf -f in.gro -o out.gro -box x y z-enlarged.
If you want a vacuum layer somwhere else, then I am afraid you will have to
write some simple program. For instance:
1)Cut your box "below" the coordinate you will want your vacuum layer to be with
editconf. Let`s assume you will change the z dimension.
2)Enlarge the z-dimension with editconf (vacuum). (prot.gro)
3)Create a water box with the same x y dimensions as above.(water.gro)
4)Change the coordinates of the water molecules so as they will be exactly above
the vacuum layer.
5)Merge the 2 files prot.gro and water.gro = vacuum .gro.
6)Don`t forget to edit the number of atoms line and the box dimensions line in
the vacuum.gro file.


Pedro Alexandre Lapido Loureiro
Laboratório de Física Biológica
Instituto de Biofísica

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