GROMACS version: 2020.2
GROMACS modification: Yes/No
Here post your question:
Is there a way to Gromacs compute a protein-ligand complex free energy value or only a de- composition of the potential energy of the system, including only nonbonded terms between the selected atom groups?
The only way to compute the free energy of a complex is with external tools, e.g. g_mmpbsa to do MM/PBSA analysis but this code is not kept updated with new GROMACS versions. Binding free energies require a series of many calculations and cannot be obtained directly from a single MD trajectory.
Short-range nonbonded terms can be decomposed via
energygrps in the
.mdp file but these quantities may or may not be physically meaningful, depending on the force field being used.
Hello and thank you Justin for your kind update:)
Is gromos54a7 force field is suitable for the short-range nonbonded energy calculation? I have seen in your tutorial charmm ff has been used.
GROMOS does not explicitly target any interaction energies in its parametrization, so no.