[gmx-users] related to box dimension : solvate protein-ligand complex

[Quyen V. Vu]

Hi,
As i know that vmd cannot understand dodecahedron, he will take 3 numbers
and plot a cubic while your box still is dodecahedron


On Fri, Jun 1, 2018, 06:48 Seketoulie Keretsu <sekekeretsu at gmail.com> wrote:

> Dear All,
>
> I am doing he Protein-ligand complex tutorial on gromacs 5.0.7 (newly
> installed). I have successfully completed this tutorial earlier on
> gromacs 4.6.
>
> After the solvation step I found out that the protein-ligand complex
> solvated system had a cubic shape while my box dimension (shown using
> vmd command: pbc box) adopted a dodecahedron like shape. Please check
> the attachment for details.
>
> What could be the possible reason behind this? Kindly advise to
> rectify the problem.
>
> The was no error or warning uptill this.
>
> Thank you.
>
> Sincerely,
>
> Seke
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