Dear all,<br><br>I am trying to solvate a protein in a dodecahedron box, and the box doesn't seem right. I tried <i>trjconv -s ur compact -pbc mol, </i>that ended up with a dodecahedron shaped water distrubution around the protein however the box is still shown as triclinic inbn Pymol? Is this Pymol's weakness or is this how dodecahedron works? Through the archive it sounds like genbox never ends up with an actual dodecahedron/octahedron box, Gromacs takes the triclinic box version to run simulation, is that right? If so how does the different box type take effect? I couldn't actually understand how does different box types are created/processed in Gromacs? <br>
<br clear="all">Thanks,<br>Nihal<br><br>-- <br>Elif Nihal Korkmaz<br><br>Research Assistant <br>University of Wisconsin - Biophysics <br>Member of Qiang Cui & Thomas Record Labs<br>1101 University Ave, Rm. 8359<br>
Madison, WI 53706<br>
Phone: 608-265-3644<br>
Email: <a href="mailto:korkmaz@wisc.edu" target="_blank">korkmaz@wisc.edu</a><br><br><br>