From: Axel Kohlmeyer (
Date: Fri Jun 12 2015 - 17:16:42 CDT

On Fri, Jun 12, 2015 at 4:51 PM, Jinasena Hewage <> wrote:
> I just want to make a PDB file containing few water molecules to insert into
> a nanotube. I tried it several ways.
> Using molefracture facility, I tried
> * Making a PDB for a single water molecule and used periodic facility to
> align several water molecules in Z direction. But I couldn't get this file
> save as PDB,
> when I save it only one molecules is there.

yes, because what is periodic is only the visualization, not the
molecular data itself.

> * Then making single molecule PDB files and add them all using tcl commands
> calling the psfgen.

huh? don't understand what you mean by that.

> Unfortunately none of these works.
> Could you please help me to do this job.

the clean strategy would be:

- get a suitable size water box (e.g. from the solvate plugin) and
make sure it is centered around the origin
- make an atom selection for a suitable cylindrical region that
contains whole water molecules
  (something like this: set sel [atomselect top "same fragment as
(name OH2 and (sqrt(x*x+y*y) < 5.0))"])
  and write out the coordinates and psf. ($sel writepdb insidecnt.pdb;
$sel writepsf insidecnt.psf)
- merge with nanotube and remove overlaps.
- setup MD, minimize
- enjoy the result.

or you can merge and remove overlaps directly using the topotools
plugin as outlined here:

and *then* remove the water molecules outside the nanotube via a
geometric criterion.


> Thank you
> Jinasena
> --
> Dr. Jinasena Hewage
> Senior Lecturer in Physical Chemistry
> (Current Position: Visiting Academic, Research School of Chemistry,
> Australian National University)
> Department of Chemistry
> University of Ruhuna
> Matara, Sri Lanka
> (+94) 071 4500 389

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.