VMD-L Mailing List
From: Jinasena Hewage (jwhewage_at_gmail.com)
Date: Sat Jun 13 2015 - 16:11:14 CDT
I was ale to get the job done.
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>
> > I just want to make a PDB file containing few water molecules to insert
> > 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
> > 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
> > 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 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