[gmx-users] how to introduce vacuum??

[Pedro Alexandre Lapido Loureiro]

> 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.

Regards,

Pedro.
--
Pedro Alexandre Lapido Loureiro
Laboratório de Física Biológica
Instituto de Biofísica
UFRJ
Brasil