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

[XAvier Periole]

Hi Peter,

Wouldn’t the exclusion act on the regular LJ and pairs add a different LJ(14)? 

With exclusions, do you have the regular LJ present?

XAvier.

> On 13 Jul 2016, at 13:17, Peter Kroon <p.c.kroon at rug.nl> wrote:
> 
> 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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