From: Jackson Cavett (
Date: Mon Jul 25 2016 - 20:34:31 CDT

Hello All,

I am currently equilibrating the integrin αVβ3 in a waterbox using NAMD.
When it is done, I would like to add some water molecules to it, but only
in the -z direction. Currently, the αVβ3 pdb and psf files have a waterbox
in which I used the following in the Tk Console (from the NAMD tutorial):

solvate myfile.psf myfile.pdb -t 5 -o myfile_waterbox

I just tried using this in the Tk Console to create my new waterbox:

package require solvate
solvate myfile.psf myfile.pdb -minmax {{-X -Y -Z} {X Y Z}} -o

with my custom waterbox dimensions, but I can't use this method when a
waterbox already exists because it creates duplicate, overlapping water
molecules. Is there a way to add water molecules a certain distance in only
one direction? Any help would be greatly appreciated!

Thank You,