[gmx-users] g_cluster problem

[Andrew Beevers]

Dear all

I am trying to produce the structure with the lowest RMSD difference to the others in the particular xtc file using g_cluster.
The problem is that the protein is in a DMPC lipid bilayer and I cannot seem to do an RMSD comparison of just the protein structure without resulting in a output structure which has no bilayer.

Is there any way of doing an RMSD comparison of just the protein structure whilst including its particular lipid environment (at that time point) in the final output structure?
Any help would be much appreciated

Thank you in advance

Dr Andy Beevers
Bioloigcal Sciences
University of Warwick
UK