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

Georgios Patargias G.N.Patargias at leeds.ac.uk
Thu May 17 14:03:17 CEST 2007


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 

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 

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

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