[gmx-users] dodecahedron box

Justin Lemkul jalemkul at vt.edu
Wed Jan 2 13:34:08 CET 2013

On 1/2/13 7:03 AM, Turgay Cakmak wrote:
> 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?

Totally normal.  Refer to the numerous posts in the list archive on this topic.



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


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