[gmx-users] Hello

[Mark Abraham]

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 
http://oldwiki.gromacs.org/index.php/Periodic_Boundary_Conditions

Mark