[gmx-users] Extend water layer along negative Z-direction

[Tsjerk Wassenaar]

Hi,

> The first thing that you need to do is to use editconf to increase your box
> z and then genbox to add more solvent. My script (and C-program) do not do
> this, they focus only on removing waters that are placed within your
> bilayer.

Of course it is also trivial to edit the .gro file and change the
third number in the last line, that indicates the z-dimension. For a
.pdb file, it's the the third number in the line starting with CRYST1.

Cheers,

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623