[gmx-users] free energy question

[Yuhua Song]

Hi,

I have a system with protein, water and ions and with one ion binded at the
binding site of protein. I intend to replace the binded metal ion with
another metal ion to calculate the free energy change. After the whole
system equilibration, I do the free energy perturbation following the manual
of Gromacs to do the free energy perturbation using the thermodynamics
method. My questions is: in preparing the *.mdp file, in the section of
energy monitoring: energygrps: I should output the whole system energy, or
protein, ions, water energy separately? which is the best way for me to
caculate the free energy perturbation caused by replacing the metal ion at
the binding site of protein?

Also, how to calculate the free energy with the g_cluster way? such as: for
the whole system, some part the protein conformation change is not big, but
some part of the protein conformation change is big. In this situation,
which is the best way for me to calculate the free energy perturbation?
g_cluster? then how to use g_cluster to realize it?

Thank you very much in advance,

Yuhua