[gmx-users] FEP with real or dummy charges?

[Georgios Patargias]

Hi 

I want to calculate the change in free energy (electrostatic contribution only)
when introducing a charge in a certain site of a protein using a single step 
FEP. 

Should this be done with charging an inserted virtual site (a dummy atom) or a 
protein atom (e.g. Ca)?  

I noticed that in the case of the dummy atom, the Coul-14:Protein-vsite zero. I am 
not sure why though...

Thanks a lot in advance for any feedback.

Best wishes 
George

Dr. George Patargias
Polymer IRC Group
University of Leeds
Leeds, LS2 9JT, UK