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

RJ rajiv at kaist.ac.kr
Fri Feb 13 13:08:06 CET 2015

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)?




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