[gmx-users] Constraints between multiple molecules

Michael McGovern mpmcgovern at wisc.edu
Thu Aug 5 11:30:42 CEST 2010

Hi everyone.  I'm doing a simulation of a protein aggregate with 3 proteins.  Ideally, I would like to constrain the distance between the center of mass of peptide 1 and the COM of peptide 2, and also constrain the distance between the combined COM of peptides 1 & 2, with the COM of peptide 3.  The pull code only allows constraints between the reference group and other groups, as far as I know.
Using constraints in the topology only allows constraints between atoms, not COM's.  This is not ideal for me, but might be acceptable.  However, constraints are only allowed within a single molecule.
Does anyone know how to deal with this problem?  Thanks a lot.

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