[gmx-users] Exclusion - determine neighboring atoms by atom indices or by bond connections?

Mark Abraham mark.j.abraham at gmail.com
Thu Jul 27 08:03:11 CEST 2017


On Wed, 26 Jul 2017 22:53 lan hoa Trinh <trinhlanhoa at gmail.com> wrote:

> Dear Gromacs community,
> In the Gromacs manual, if nrexcl = 3, that means atoms i+1, i+2, i+3 are
> excluded from non-bonded interactions with atom i. I don't know how Gromacs
> determine the neighboring atoms, based on atom indices or bond connections?

Every mention of nrexcl in the reference manual specifically mentions that
it refers bonded connectivity. Atom indices couldn't work. What were you

For example, if I have a simple connection between CA and CB atoms like the
> following
> CA(1) -------------CA(3)---------------CA(5)----------------CA(7)
> |                       |                         |                     |
> CB(2)              CB(4)                CB(6)               CB(8)
> Indices of atoms are shown in the brackets. If the neighbouring atoms are
> determined based on atom indices, that means CB(2) will not form non-bonded
> interactions with CA(3), CB(4),CA(5) but still form non-bonded interactions
> with CA(1), that is what I don't want since CB(2) and CA(1) already form
> bonded interaction (harmonic bond energy)

The implementation works to exclude nonbonded interactions with bonded
neighbours in all directions. The most convenient way of expressing and
implementing it is to loop over all atoms with index i and exclude all
bonded neighbours whose atom indices are greater than i. Excluding the
interaction between i and atoms with smaller indices were handled when
considering those atoms.


It really confused me. I am looking forward to hearing from you.
> Thank you very much in advance.
> Best regards,
> *Lan Hoa*
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