[gmx-users] center of mass removal

[Li Qiang]

Dear all,

I am simulating short peptide in GROMACS. Center of mass need to be
removed to keep the peptide from jumping out.

I have two questions about this:
1, when I remove COM of the peptide using comm_grps, do I need to put
the solvent(including the counter ion) at the same time for COM removal?
or the program will take care of the whole system automatically? 
2, Can anybody tell how the COM removal is achieved (in gromacs or other
methods available)?

thank you

Qiang