[gmx-users] pls help me with the interaction energy!

David van der Spoel spoel at xray.bmc.uu.se
Wed May 26 09:32:57 CEST 2004

On Wed, 2004-05-26 at 06:20, Jinzhi Tan wrote:
> 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.

check the archives.
> Best wishes, 
> lily tan
> 2004-5-25
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone:  +46 18 471 4205  fax: +46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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