[gmx-users] free energy calculation using TI

[Zhale Ghaemi]

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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