[gmx-users] how big the difference between two ligand can FEP handle?]

[QZ]

Dear All,
 I am learning to use FEP to get the bind free energy difference between 
two totally different ligands bound a protein. The number of atoms 
varies between the ligands. Does gromacs require the same number of 
atoms between sytem A and B? If not, how does the interpolation work 
between the ligands with different atom numbers? Should I use dummy 
atoms to match the atom numbers between the ligands? Thanks for any input.

Q. Zou , Ph D.
Indiana University



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