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

Seketoulie Keretsu sekekeretsu at gmail.com
Fri Jun 1 01:47:50 CEST 2018

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.



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