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

[Peter Kroon]

Hi Xavier (and list),

I think that's a good way of rephrasing my question ;)
Anyway, I made a mock system with just 2 particles (included below).
gmx dump'ing the two tprs (with and without exclusions) I can't tell the
difference, apart from the number of exclusions generated:

>>> diff dump_no_excl dump_with_excl
1c1
< no_excl.tpr:
---
> with_excl.tpr:
12c12
<    ld-seed                        = 4213247321
---
>    ld-seed                        = 2241521802
221,223c221,223
<          nra=2
<          excls[0][0..0]={0}
<          excls[1][1..1]={1}
---
>          nra=4
>          excls[0][0..1]={0, 1}
>          excls[1][2..3]={0, 1}

I ran this mock-system with a simple energy minimization. Since the
pairs directive gives both particles an identical charge I expect them
to drift apart if pairs > exclusions.
And indeed this is what vmd shows, so it seems that exclusions only work
on "normal" LJ (and coulomb?) interactions, and not specific pairwise
interactions.
I'm hoping someone with intimate gromacs knowledge can still
confirm/deny this though, I'd rather not dig through the code.

And my mock-topology:
[ moleculetype ]
blab 0

[ atoms ]
1   Qd  1   VAL A   1   0;
2   P5  1   VAL B   2   0;

[pairs]
1 2 2 0.1 -0.4 -0.4 0 1.0e-06

#ifdef EXCL
[exclusions]
1 2
#endif

[ system ]
blub

[ molecules ]
blab 1


Peter


On 13/07/16 14:03, XAvier Periole wrote:
> 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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