[gmx-users] dodecahedron, octahedron box

E. Nihal Korkmaz enihalkorkmaz at gmail.com
Sat Jul 9 00:10:55 CEST 2011

Dear all,

I am trying to solvate a protein in a dodecahedron box, and the box doesn't
seem right. I tried *trjconv -s ur compact -pbc mol,  *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?


Elif Nihal Korkmaz

Research Assistant
University of Wisconsin - Biophysics
Member of Qiang Cui & Thomas Record Labs
1101 University Ave, Rm. 8359
Madison, WI 53706
Phone:  608-265-3644
Email:   korkmaz at wisc.edu
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