[gmx-users] dodecahedron box

Turgay Cakmak turgaycakmak34 at gmail.com
Wed Jan 2 13:03:38 CET 2013

Dear gromacs users,

I am trying to solvate several peptides (at a desired positions) in a
dodecahedron box. I have done following steps;

   1)   editconf -f peptides.gro -o peptides_nb.gro -c -d 1.0 -bt dodecahedron
   2)   genbox -cp peptides_nb.gro -cs -o peptides_solv.gro -p topol.top
   3)   After adding ions, I did energy minimization.
   4)   trjconv -f minim.trr -pbc mol -ur compact -o trajout.gro -s minim.tpr

After that, I looked the system in VMD: Water molecules are around the
peptides in the dodecahedron shape. But, box still seems like a
rectangular shape. Is it correct or am I doing something wrong?

Thanks in advance,

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