VMD-L Mailing List

From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Mon Jul 28 2008 - 06:52:08 CDT

1) this script will solvate in water cube of the size 50x50x50, but
your protein must be placed in the center first.

package require solvate
solvate myfile.psf myfile.pdb -minmax {{-25 -25 -25} {25 25 25}} -o
myfile_watercube
exit

2) if you use instead

solvate myfile.psf myfile.pdb -t 5 -o myfile_waterbox

then the system will be solvated in water box (box, not cube, i.e.
with different length, width and height) with guaranteed 5A thickness
of water layer between the box boundaries and min/max coordinates of
the protein.

3) padding is the thickness of water between protein and water boundaries.

if padding is zero, then the protein will touch the boundary of the
solvation box on each side.

On Mon, Jul 28, 2008 at 2:25 AM, Sue Legge <sue.legge_at_rmit.edu.au> wrote:
> A couple of questions regarding solvating a peptide in a cubic box with periodic boundary conditions,
>
> what exactly is the padding?
>
> is it possible to specify an exact box size? Eg. can I create a box 50x50x50 angstrom?
>
> also, is there some way to measure the exact size of the box?
>
> thanks
> sue
>
> ____________________
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> Applied Physics
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-- 
Roman Petrenko.
Physics Department
University of Cincinnati