[gmx-users] "alchemical" transformation

[Cristian Danciulescu]

Dear gromacs users,
Free energy differences between two systems A and B 
(aminoacids) can be calculated perturbing some parameters 
(masses, bonded and non-bonded interactions) in order to change 
the structure A to B.
Some of the proper dihedrals that must be perturbed in the 
transformation A->B have different multiplicities. But multiplicities 
can not be perturbed during the free energy calculations. 
Could someone tell me how to solve or avoid this problem?
Thank you,
Cristian