[gmx-users] solvate protein in water?

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Oct 27 06:50:07 CEST 2005

Hi Zhen Qi,

It's not the shape that counts, it's the lattice vectors. In fact any box
can be represented in any way, most notably as a rectangular unit cell,
which has computational advantages. Check the manual on periodic boundary
conditions. It's well explained there. If you want to visualize your
triclinic box, you can use trjconv with the options -ur tric -pbc inbox
Although it's probably nicer to visualize it as a hexagonal prism, which is
what you should get when using trjconv with -ur compact -pbc inbox



On 10/26/05, Zhen Qin <zhen at hec.utah.edu> wrote:
> Hi,
> I met a problem with solvating my protein inside water molecules.
> My protein is inside a triclinic box (with alpha=90, belta=90, and
> garma=60), and the box-vectors satisfy the GROMACS' requirements. I use
> "genbox -cp protein.pdb -cs spc216.gro -o out.pdb". But I found in
> out.pdb, the box's shape has been changed to cubic. That is not what
> I've expected. I have hoped that water molecules are added to the
> triclinic box and solvate the protein. In genbox's options, the "vector"
> option is only for the length of each box's vector, not including the
> angles. How could I specify the angle?
> Is there any way to solvate a protein in a non-cubic box?
> Thanks alot.
> -Zhen
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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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