From: Axel Kohlmeyer (
Date: Thu Sep 05 2013 - 13:38:51 CDT

On Thu, Sep 5, 2013 at 6:40 PM, Ali Alizadeh <> wrote:
> Dear All users,
> I want to add a gap between my surface and molecular environment. Are ther
> any options in vmd
> for performing this? Or Can I add a gap wherever in my simulation box? I
> want to omit the
> interactions between them, my surface(crystal) and molecules. I want to
> ready a input
> for lammps.

if you want to disable the interactions, you don't need a gap, only
exclude those interactions from the neighborlist. LAMMPS allows you to
do that.

if you *do* need a gap anyway, you need to learn how to write a VMD/Tcl script.
you need to create an atom selection for your surface atoms. you can
translate those with a command that you give to the generated
atomselect function. then you need to adjust the box dimensions and
save the configuration. of course, this description is shorthand. you
will have to look up the details in the VMD user's guide and start
with some simple test system with only a few atoms, to figure out the
script. once you understand the principles, you can write the script
you need for your full task. if you try any shortcuts, it will take
longer (i know that nobody believes that, but i say it now, so i can
later say that i said it at the beginning).


> --
> Sincerely
> Ali Alizadeh

Dr. Axel Kohlmeyer
International Centre for Theoretical Physics, Trieste. Italy.