[gmx-users] Ligand coming out while trying Drug-enzyme tutorial

[Tsjerk Wassenaar]

Hi Vivek,

> Now when I am processing the modified .gro file to generate box, the ligand
> and cofactor are going away from the protein molecule and I am not able to
> analyze the complex.

Gradually going away, or suddenly jumping?

In the latter case, read up on periodic boundary conditions.

Tsjerk

-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist