[gmx-users] protein falls apart in energy minimization

[Mark Abraham]

Zhong Zheng wrote:
> hi all
> 
> I am running Gromacs on a protein consisted of three chains. But no 
> matter how I tried, the protein always falls into three parts 
> (corresponding to each chain) after a simple 2000 steps energy 
> minimization. Can anyone help me please? Thanks.

Are you seeing a visualization artefact caused by periodic boundary 
conditions? You can play with trjconv on your output file to see.

Mark