[gmx-users] Doubt about Free Energy Calculations using g_bar

[Varvdekar Bhagyesh Rajendra]

Dear all,

I am attempting to find Binding affinity of a Protein-ligand system by following the Free Energy tutorials (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html). 
It says : "The procedure in this tutorial essentially assumes that charges have been properly been turned off prior to this point". How do we turn off the charges of a group specified in an index file (the ligand in my case) ?


Thanking in anticipation,

Best Regards,

Bhagyesh