[gmx-users] about interaction energy

Jinzhi Tan jztan at mail.shcnc.ac.cn
Mon May 24 09:36:49 CEST 2004

Dear gmx-users,

I have two questions.
First question is about protein-protein interaction. The protein is a dimer containing chain A and chain B. Can I get the interaction energy by just calculating potential energy of the whole protein (Eab), chain A (Ea) and chain B (Eb), then interaction energy equals to  Eab-Ea-Eb? When I do this, I extract the xtc file of chain A (or B)and define A (or B)as the energy group in the mdp file. I wonder whether I am right or not. If I am right, can I get the LR coulomb energy by using the formula of E(interaction energy)-E(interaction LJ energy)-E(interaction SR coulomb energy)? How can I deal with the charge?

Second question is about protein-ligand interaction. If I just calculat the interaction energy between ligand and one residue of the protein, I can define the ligand and the residue as the energy groups in mdp file (as many lists mentioned before). But in doing so, I just get the LJ and SR coulomb interaction energy since I use PME. I wonder if the LR coulomb interaction energy may large or not? Can I just add  the LJ and SR coulomb interaction energy to represent the whole interaction energy?

Thank you for any answers.

Best wishes, 


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