VMD-L Mailing List

From: Jinasena Hewage (jwhewage_at_gmail.com)
Date: Sat Jun 13 2015 - 16:11:14 CDT

Thanks Axel,
I was ale to get the job done.
Hewage

On Fri, Jun 12, 2015 at 6:16 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Fri, Jun 12, 2015 at 4:51 PM, Jinasena Hewage <jwhewage_at_gmail.com>
> 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:
>
>
> https://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---various-tips-tricks#TOC-Combine-multiple-data-files-with-overlap-detection-and-removal
>
> and *then* remove the water molecules outside the nanotube via a
> geometric criterion.
>
> axel.
>
>
>
> >
> > 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 akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
> 

-- 
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