[gmx-users] how big the difference between two ligand can FEP handle?]
qzou at iupui.edu
Mon Sep 29 04:02:01 CEST 2003
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.
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