VMD-L Mailing List

From: James Kress (jimkress_58_at_kressworks.org)
Date: Mon Jul 25 2016 - 22:00:08 CDT

Can’t you just specify minmax so that min is the largest (in magnitude) -Z you want and max is a Z value at the minimum Z border of your existing box?

 

Jim

 

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From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Jackson Cavett
Sent: Monday, July 25, 2016 9:35 PM
To: vmd-l <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: Custom Water Box

 

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