[gmx-users] energy contributions

Mark Abraham mark.abraham at anu.edu.au
Thu Jul 8 07:38:29 CEST 2010

----- Original Message -----
From: jojo J <joojoojooon at gmail.com>
Date: Thursday, July 8, 2010 13:17
Subject: [gmx-users] energy contributions / question about solvating
To: gmx-users at gromacs.org

> Hello everyone,
> I have a question on LJ and coulomb 1-4 energy terms. These are considered as intramolecular interactions and LJ and coulomb SR as intermolecular. If nrexcl in top file is 3, this means we obtain 1-4 energies, 1-5, 1-6,.... Now what we calculate as intermolecular (SR) contributions includes 1-5, 1-6,.. right? and 1-4 are listed separetely in g energy list.

Yes. Crafty use of energy groups will make this clear, but that's not a scalable solution if you want to look at (say) 1-5 interactions in multiple different molecules that have such interactions, since you can only have 256 energy groups.
> so to get energies between particles one needs to ecxlude 1-5, 1-6 ...on each molecule?

Look at using energy groups and energy group exclusions.

> also I would like to know what is specefic with 1-4 interactions, whay are they listed separately. I mean why do we have not 1-5 for instance?

Historically, people parameterizing found that 1-5 (and larger) interactions worked OK as they still are, but that 1-4 needed various compromises. In part, that's because they interact with the dihedral on those atoms. The common forcefields have various approaches in this regard, and GROMACS manages to cater to all of these.


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