- #1
MichaelWiteman
- 10
- 1
Hi,
To compute, for example, the Gibbs energy change for a ligand binding to a protein, various so called alchemical methods are used in molecular dynamics simulations. My question is why can't we just obtain averaged Gibbs energies for 1) the free ligand and protein in the same water box, and 2) the protein-ligand complex in the water box and then subtract? Both cases will have the same amount and type of atoms and the simulation would be conducted at the same temperature, density etc. I know this is a naive question but understanding the reasons why this is not done will help me understand a few things.
Thanks!
--Mike
To compute, for example, the Gibbs energy change for a ligand binding to a protein, various so called alchemical methods are used in molecular dynamics simulations. My question is why can't we just obtain averaged Gibbs energies for 1) the free ligand and protein in the same water box, and 2) the protein-ligand complex in the water box and then subtract? Both cases will have the same amount and type of atoms and the simulation would be conducted at the same temperature, density etc. I know this is a naive question but understanding the reasons why this is not done will help me understand a few things.
Thanks!
--Mike
