[gmx-users] calculating interaction energies of dimers and ligand

[RJ]

Dear all,


I need to calculate the interaction energy (Column SR & LJ SR) of chain A with chain B. 


Should I need to select the specific interacting residues to between chain A and B ? Also to chain C ( Ligand molecule)?. I used the gmx energy command line but there are index.ndx option to indicate the group of residues so?


Also, how do i calculate the interaction energies in nano second time scale ( seems there is no -tu option in gmx energy)?




Thanks


Regards


RJ