[gmx-users] dodecahedron box

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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