[gmx-users] free energy calculations

[Ragothaman Yennamalli]

Hi,
I want to run free energy calculations on a particular protein-ligand
complex. I do not have much knowledge on this so I have some questions,
hopefully someone might give me clear answers.
I am following the tutorial given in this link:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/08_advanced.html

My questions are as follows:
1. I am assuming that I do not need the "protein without the ligand" form
for free energy calculations. Am I right?

2. To use g_bar, I need to run the protein-ligand complex with
    a) first with lambda ranging from 0.5 to 1 for vdw coupling and
    b) followed by lambda ranging from 0.5 to 1 for coulombic coupling
Adding these would give the deltaG I am looking for. Am I right?

3. Are there any papers that use g_bar function in gromacs to calculate free
energy?

Thanks in advance,
Raghu
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