VMD-L Mailing List

From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed Jan 12 2011 - 10:59:34 CST

Hi Francesco,

To make a truncated octahedron box:

a) create a large cubic box of water containing the truncated octahedron
b) create a water selection for the truncated octahedron: you can
select water from a selection based on its position with respect to a
truncating plane. Here is an exemple:

set mywater [same residue as (name OH2 and x + y + z > 100 and 2x - y
+ z < -42)]
This will select water based on two planes whose equations I just made up.

c) save that selection to disk:
$mywater writepdb box.pdb

Cheers,
Jerome

On 12 January 2011 11:43, francesco oteri <francesco.oteri_at_gmail.com> wrote:
> Dear vmd users,
> I need to solvate my system into a Truncated octahedron box to run a
> simulation using namd with charmm force-field.
> I checked the mailing list and also the web, but seems that nobody knows how
> to solve the problem.
> Any suggestion?
> Is There a way to obtain Truncated octahedron Box from a cubic box?
> Thanks