VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jul 14 2011 - 15:29:08 CDT

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.