VMD-L Mailing List

From: Ali Alizadeh (ali.alizadehmoj_at_gmail.com)
Date: Thu Sep 05 2013 - 14:41:00 CDT

Dear Axel,

Thank you very much for your reply.

Yes, You are right about understanding the principles but sometimes there
is no patience for doing this.

On Thu, Sep 5, 2013 at 11:08 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Thu, Sep 5, 2013 at 6:40 PM, Ali Alizadeh <ali.alizadehmoj_at_gmail.com>
> 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 system.data 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).
>
> axel.
>
>
> >
> > --
> > Sincerely
> >
> > Ali Alizadeh
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
> 

-- 
Sincerely
Ali Alizadeh