From: Axel Kohlmeyer (
Date: Fri Nov 11 2011 - 13:27:35 CST

On Fri, Nov 11, 2011 at 1:31 PM, niaz poorgholami <> wrote:
> Dear all
> I have a pdb file for carbon nanotube and a pdb file for polymers and I
> want to place polymer molecules on a surface of CNT. I can move polymers
> by VMD main/mouse/move but I want to locate polmers in a appropriate
> position with respect to
> CNT surface and then save the created structure. would you please help me
> how to place polymers and then save
> that ?

VMD is not a good tool to do that.
better would be to place your polymers
somewhere in space, eg. using a tool
like packmol and then pick one or more
reference points on them and use slowly
growing restraints or steered MD to gently
pull them where you want them to go.


>                     niaz

Dr. Axel Kohlmeyer
College of Science and Technology
Temple University, Philadelphia PA, USA.