GROMACS version: 2023
GROMACS modification: Yes/No
There are many different ways aptamers can bind to proteins. In other words, there are multiple bound complex configurations. To test the binding affinity (free energy) of each configuration, is it possible to slightly displace the aptamer in each configuration slightly apart from the protein, and run a MD simulation using GROMACS to see how well the aptamer binds back to the protein in this configuration either through a binding free energy value or other parameter(s)/output(s) that measure binding stability?