Hi Apramita, Up to my knowledge, It is not necessary to keep the peptide at the centre due to the periodicity you can have 'continues' motion throughout the simulation. But, it is always better to keep it in convenient positions to avoid any artefacts. Further, I don't have any idea about your simulation system, whether it contains lipid layers or any other proteins and what kind of motions/diffusions your expecting. -- Gromacs Users mailing list
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