[gmx-users] Should the peptide be centered initially in the box if we want to calculate its diffusion later?

[Nikhil Maroli]

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.