[gmx-users] [pairs] vs [exclusions]
Peter Kroon
p.c.kroon at rug.nl
Thu Jul 14 10:43:43 CEST 2016
Hi Mark,
thanks for the elaborate answer.
If [pairs] are considered bonded interactions it's perfectly clear.
Peter
On 13/07/16 17:24, Mark Abraham wrote:
> Hi,
>
> Maybe I missed the point earlier, but as e.g. 5.4.4 Exclusions section of
> PDF reference manual says:
>
> "Extra exclusions within a molecule can be added manually in a [ exclusions
> ] section. Each
> line should start with one atom index, followed by one or more atom
> indices. All *non-bonded*
> interactions between the first atom and the other atoms will be excluded."
>
> Non-bonded interactions don't exist until after you've measured the
> distance between the particles and found that they're within the cutoff.
> Adding an exclusion (howsoever generated) says "look, it doesn't matter,
> these particles don't have a non-bonded interaction ever."
>
> The preceding section talks about *intramolecular* [pairs], which are
> organized as one of the kinds of bonded interaction. Those just get
> computed - whatever [exclusions] says doesn't matter.
>
> If so, then you can show that it works that way by taking a molecule (e.g.
> capped alanine) where nrexcl is low enough that the automatic generation of
> bond-based exclusions doesn't apply for some pair of atoms, and computing a
> potential energy. Add an [exclusions] between two atoms to observe that the
> nonbonded energy changes. Then add [pairs] as well on the same atoms, to
> show the total energy restored, but now in a different component.
>
> Mark
>
> On Wed, Jul 13, 2016 at 4:04 PM Peter Kroon <p.c.kroon at rug.nl> wrote:
>
>> 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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