VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Sep 05 2013 - 14:42:28 CDT

On Thu, Sep 5, 2013 at 9:41 PM, Ali Alizadeh <ali.alizadehmoj_at_gmail.com> wrote:
>
> 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.

but mark my words: you *will* suffer for cutting corners. there ain't
no escape from the blues.

axel.

>
>
> 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 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.