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

lan hoa Trinh trinhlanhoa at gmail.com
Wed Jul 26 22:52:43 CEST 2017

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?
For example, if I have a simple connection between CA and CB atoms like the

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)

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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