VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jan 15 2003 - 10:29:36 CST

Dear Ioana,
  There's a tutorial that shows how to do some of this located
on the NAMD web site here:
  http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/

One of the examples in the tutorial involves building a hexagonal
volume of water. Jim (main developer of NAMD) suggested that this
would be a good starting point for what you have in mind.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jan 14, 2003 at 06:05:46PM -0800, Ioana Cozmuta wrote:
> Dear VMD-users,
>
> I have a cylindrical pore and I want to add water only inside the pore.
> I did create in vmd a psf file corresponding to my initial pdb structure
> and also used the minmax procedure to calculate the extremes of the pore.
> then I just used the solvate extension in vmd
> solvate <psffile> <pdbfile> -o new -minmax { {minvalues} {maxvalues}}
>
> Indeed there were water molecules added but the whole pore is now inserted
> into a big box. Is there an additional option that I can use to tell VMD
> to add waters only inside the xmin, ymin, zmin, xmax, ymax, zmax of the
> pore and not to add any outside it?
>
> Thank you in advance,
> Ioana
>
> ****************************************************************************
> * Ioana Cozmuta, PhD * *
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