[gmx-users] protein falls apart in energy minimization

Mark Abraham Mark.Abraham at anu.edu.au
Tue May 12 06:43:29 CEST 2009

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.


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