[gmx-users] [pairs] vs [exclusions]

[Mark Abraham]

Hi,

I don't know which acts first, but making a few such .tpr files and
(hopefully) gmx check on them should make clear what happens. Or worst case
gmx dump the .tpr and do a textual diff. You can probably make your life
easier by playing around with atoms with high indices.

Mark

On Wed, Jul 13, 2016 at 10:46 AM Peter Kroon <p.c.kroon at rug.nl> wrote:

> Dear list,
>
> I a have a short question on topologies, and the manual is somewhat
> unclear.
> If I have a topology which defines both an exclusion between an atom
> pair and a specific interaction between them using the [pairs] directive
> (function type 2), will they then have a non-bonded interaction, or not?
>
> Thanks in advance,
> Peter Kroon
>
> PS.
> short example topology:
>
> [ moleculetype ]
> my_molecule 1
>
> [ atoms ]
> ...
>
> [ pairs ]
> 1   4   2   .....
>
> [ exclusions ]
> 1   4
>
> [ bonds ]
> no bond between 1 and 4
>
> ...
>
> --
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