Dear all, I have a covalently bond ligand to a protein which its c=c bond could stay in Cis-enamine or Trans-enamine (I relaxed the structures of those two using classical MD in Gromacs4). I'm calculating the free energy difference of the Cis and Trans states using thermodynamic integration implemented in Gromacs4. Besides the dihedrals of Cis and Trans that are specified in the topology file (so Gromacs should undersatnd it should rotate around the specific bond gratually), I would like Gromacs consider both Cis and Trans coordinates when it is calculating the potential of mean force. How can I make it accept the two coordinates at the same time? Thanks in advance, Zhaleh
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