TI - Free Energy - couple-intramol=no

[havc93]

Hello, I have a related question below and greatly appreciate your feedback.

Free energy calculation for DNA-protein binding

GROMACS version: GROMACS modification: No Here post your question I am trying to do alchemical methods according to the following cycle (link below) to calculate the absolute binding free energy of a protein binding to DNA. However I get the following error whenever trying to do energy minimization https://alchemistry.org/wiki/Absolute_Binding_Free_Energy_-_Gromacs_2016 Fatal error: There are 1315162 perturbed, excluded non-bonded pair interactions beyond the pair-list cut-off, which is n…