[gmx-users] Ligand is moving far away after energy minimization

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 20 04:20:55 CET 2009

Ms. Aswathy S wrote:
> Dear Gromacs users,
> I am doing the MD of protein ligand complex. When I did the energy minimization of this complex,   in the result , the ligand molceule is moving far away from the protein.
> What could be the possible reason? can anyone tell me how can i overcome this?

Two possibilities come to my mind.

1. The parameters of the ligand are inappropriate, causing the ligand to be 
ejected from the active site.  This is unlikely in a simple EM procedure, and 
probably would cause lots of LINCS or "blowing up" warnings.

2. More likely: Your protein is positioned near a box edge and the ligand is 
crossing periodic boundaries.  Consider how you set up the box and read about PBC:



> Thanks in advance.
> Aswathy
> Amrita School of biotechnology
> Dept. Biotechnology
> Ext. 3108
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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