Hi Zhen Qi,<br>
<br>
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<br>
<br>
Cheers,<br>
<br>
Tsjerk<br><br><div><span class="gmail_quote">On 10/26/05, <b class="gmail_sendername">Zhen Qin</b> <<a href="mailto:zhen@hec.utah.edu">zhen@hec.utah.edu</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi,<br> I met a problem with solvating my protein inside water molecules.<br> My protein is inside a triclinic box (with alpha=90, belta=90, and<br>garma=60), and the box-vectors satisfy the GROMACS' requirements. I use<br>
"genbox -cp protein.pdb -cs spc216.gro -o out.pdb". But I found in<br>out.pdb, the box's shape has been changed to cubic. That is not what<br>I've expected. I have hoped that water molecules are added to the<br>
triclinic box and solvate the protein. In genbox's options, the "vector"<br>option is only for the length of each box's vector, not including the<br>angles. How could I specify the angle?<br>Is there any way to solvate a protein in a non-cubic box?
<br><br>Thanks alot.<br><br><br>-Zhen<br>_______________________________________________<br>gmx-users mailing list<br><a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
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</a>.<br></blockquote></div><br><br clear="all"><br>-- <br><br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>
Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>