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

[Peter Kroon]

Hi Mark (and list),

thanks for the ideas.
`gmx check -s1 with_excl.tpr -s2 no_excl.tpr` didn't tell me much,
unfortunately:
...
comparing blocka excls
excls.nra (1944 - 1920)
comparing groups
...

I think this means that with_excl.tpr contains 22 more exclusions.

Running gmx dump on both files shows that both list the relevant `LJC-14
q` entries. However, with_excl.tpr also produces the appropriate exclusions.

So which takes precedence? From these results I'm tempted to think the
exclusions take precedence, otherwise they wouldn't end up in the tpr.
Or does mdrun do something intelligent here?

Peter


On 13/07/16 12:18, Mark Abraham wrote:
> 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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