[gmx-users] dodecahedron, octahedron box

Justin A. Lemkul jalemkul at vt.edu
Sat Jul 9 00:17:48 CEST 2011

E. Nihal Korkmaz wrote:
> 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 

That's how it works, really.  Processing with trjconv reconstructs the desired 
unit cell shape, but all the box information ever used by Gromacs (and other 
software programs) is still the triclinic cell.

> 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?

Start with reference 18 of the manual, where this is discussed.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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