Hi Alex,
The free energy does depend on volume
Thus, you should simulate bound and free state with the same volume.
However, this is not necessary, since the error is pretty small usually (in my
experience)
Here two references:
H?nenberger, Philippe H., and J. Andrew McCammon. "Effect of artifi
Have you had a look at
http://www.alchemistry.org/wiki/GROMACS_4.6_example:_n-phenylglycinonitrile_binding_to_T4_lysozyme
to see if that technique would be applicable to you and look through
the references given? When you do absolute transformations you will
need to think about standard state (an
