VMD-L Mailing List

From: Anna (mol.dynamics_at_yahoo.com)
Date: Thu Jul 14 2011 - 17:17:56 CDT

Dear Dr Axel,

Thank you so very much for the valuable suggestion, I was able to do what I wanted! Thank you!

With best wishes,
Anna

On 14 Jul 2011, at 21:29, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Thu, Jul 14, 2011 at 4:22 PM, molecular dynamics
> <mol.dynamics_at_yahoo.com> wrote:
>> Dear all LAMMPS & VMD experts/users,
>>
>>
>> I would like to create new topologies for polymers -- I am familiar with
>> topotools and use it regularly to create several polymer chains. Now I
>> would like to create polymer chains such that the copy of my initial
>> polymer chain is not only translated but also tilted (say one 35
>> degrees, another 90 etc.). Is there possibly a way to do this? I'd be
>
> yes. this can be done internally with VMD scripting.
> you can create an atom selection for a given copy of
> a chain and then apply the "move" command.
>
> http://www.ks.uiuc.edu/Research/vmd/current/ug/node120.html#6477
>
> now all that is left is to construct the 4x4 transformation matrix,
> but that should be easy to find in a text book or on the web.
>
> cheers,
> axel.
>
>> pleased even if there was a way to generate the coordinates in .xyz
>> format, which I could easily convert into lammps format.
>>
>> Thank you very much for your time and attention!
>>
>> With best wishes,
>> Anna
>>
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>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.