[gmx-users] how to fill water molecules only in required place

[Santan William]

Hey gmx users,
       I just began studying gmx, here is a basic question irritating me.
There is a methanol.pdb ( box size: 23.619 23.619 23.619) in tutor, I want
to put a same size water box on the right side of methanol box to simulate
the mixing process. I know there is a mix.pdb file in tutor already, but I
want to create it by myself.  When I use genbox :
genbox -cp methanol.pdb  -cs spc216 -o mix.pdb -box 4.7238 2.3619 2.3619

1. The problem is, in created mix.pdb file, some water molecules always
inserted in methanol box. How can I just create a pdb file of left methanol
box only contains methanol and  right water box only contains water?


2. If use "genbox -cs spc216 -o water.pdb -box 2.3619  2.3619 2.3619" to
create a water box, how can I get a configuration which the first atom's
coordinates are 0 0 0?

Thanks in advance.

William
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