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From: Jackson Cavett (jcavett_at_mail.bradley.edu)
Date: Mon Jul 25 2016 - 20:34:31 CDT
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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
myfile_watercube
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,
Jack
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