Mark.Abraham at anu.edu.au
Tue Jul 14 08:37:24 CEST 2009
nikhil damle wrote:
> I am carrying out energy minimization of the protein peptide complex.
> But even after using nstcomm=1 and/or pbc=xyz, my energy minimized
> structure has peptide far away from the binding site. This did not
> happen with ATP-protein complex. Even in Drug-enzyme tutorial, similar
> .mdp file is given for energy minimization. What could be possible
> reasons for such flying away of the peptide ? How should I fix the problem ?
Please use a descriptive subject line, not a generic greeting.
You are probably seeing a periodicity artefact. See
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