Hi gromacs users,
I have succeeded in placing two polypeptides in a box.
However my objective is to model the interaction between the central alpha
c-atoms of both molecules. In particular the distance between them.
My question is how do I implement distance between them before simulation,
as the molecules seem to be stuck together when I checked the pdb file.
I would also appreciate advice on how to get the results after simulation,
i.e the distance between the central alpha c-atom and the atoms of the other
molecule.
Regards
John
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