[gmx-users] about interaction energy

Anton Feenstra feenstra at chem.vu.nl
Wed Jun 2 17:47:17 CEST 2004

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?

Most simple is to define Chain A and Chain B as separate groups in an .ndx
file, and specify 'energy_grps = ChainA ChainB' in your .mdp file. Then, there
will be groups in your energy (.edr) file with the internal energies for the
chains, but also for the respective interaction energies.

> 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?

No - the coulomb part can be a significant contribution. There is a trick to
resolve this using PME, by re-calculating energies with charges set to zero
for some groups of atoms. This involves a few runs of grompp with options and
mdrun -rerun. This has been described a few times on this list by David van
der Spoel (IIRC), you can search the list on the website. (by the way, this
issue of PME energies applies equally to the protein-protein interaction
energy you ask about in your first question).


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |

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