[gmx-users] Polypeptide interaction

[Erik Lindahl]

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  
outside gromacs.

> 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.

g_dist

Cheers,

Erik