Hi,<br>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. <br>I am following the tutorial given in this link: <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/08_advanced.html" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/08_advanced.html</a><br>
<br>My questions are as follows:<br>1. I am assuming that I do not need the "protein without the ligand" form for free energy calculations. Am I right?<br><br>2. To use g_bar, I need to run the protein-ligand complex with <br>
a) first with lambda ranging from 0.5 to 1 for vdw coupling and <br> b) followed by lambda ranging from 0.5 to 1 for coulombic coupling <br>Adding these would give the deltaG I am looking for. Am I right?<br><br>3. Are there any papers that use g_bar function in gromacs to calculate free energy? <br>
<br>Thanks in advance,<br>Raghu<br>