[gmx-users] Polypeptide interaction
lindahl at cbr.su.se
Mon May 28 16:22:37 CEST 2007
On May 28, 2007, at 4:01 PM, Sheyore Omovie wrote:
> 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.
If you mean moving the molecules wrt each other, that has to be done
> 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.
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