Free energy calculations using organometallics

User discussions
1

GROMACS version: 2020
GROMACS modification: No
Hello all,

Has anyone got experience calculating free energies from molecular dynamics simulations involving enzyme/organometallic ligand complexes? I appreciate these are niche/uncommon systems and therefore may not have been explored before. I was considering using gmx_MMPBSA but there may be issues defining Ag radii and therefore was interested in potential alternatives if anyone has suggestions.

Thank you in advance
Sam

2

I would use (well tempered) funnel metadynamics. You’ll have to patch your GROMACS code with PLUMED, but there are plenty of literature examples and nice tutorials on the PLUMED website.

There is also FEP. I’ve never used it, but i believe there is a tutorial on mdtutorials.