[gmx-users] genconf and bonded interactions
Justin A. Lemkul
jalemkul at vt.edu
Wed Jul 27 15:38:26 CEST 2011
Please make sure to keep the discussion on the list.
Fabio Affinito wrote:
> Justin,
> first of all, I thank you very much for your help: it's very precious. I
> regret I didn't notice before the molecule was broken.
I suggested to you yesterday that your initial configuration was broken. You
told me it wasn't.
> Unfortunately the problem is not solved with your recipe. I used trjconv
> on the starting configuration and then I used the genconf.
> The mdrun fails with the same error. In this case, the atoms involved in
> the error are not the same of the previous one. But once again the bond
> length is completely odd.
> During the grompp I had some warning, but I can't understand where they
> are coming from:
>
Certain bonded interactions can't take place between massless particles. As the
warning states, if pdb2gmx produced the topology, don't worry about it.
>> Cleaning up constraints and constant bonded interactions with virtual
>> sites
>> Removed 1305 Angles with virtual sites, 6251 left
>> Removed 480 Proper Dih.s with virtual sites, 363 left
>> Converted 2230 Constraints with virtual sites to connections,
>> 2596 left
>> Warning: removed 582 Constraints with vsite with Virtual site 3out
>> construction
>> This vsite construction does not guarantee constant bond-length
>> If the constructions were generated by pdb2gmx ignore this
>> warning
>> Cleaning up constraints and constant bonded interactions with virtual
>> sites
>> Removed 1305 Angles with virtual sites, 6251 left
>> Removed 480 Proper Dih.s with virtual sites, 363 left
>> Converted 2230 Constraints with virtual sites to connections,
>> 2596 left
>> Warning: removed 582 Constraints with vsite with Virtual site 3out
>> construction
>> This vsite construction does not guarantee constant bond-length
>> If the constructions were generated by pdb2gmx ignore this
>> warning
>> Cleaning up constraints and constant bonded interactions with virtual
>> sites
>> Removed 1305 Angles with virtual sites, 6251 left
>> Removed 480 Proper Dih.s with virtual sites, 363 left
>> Converted 2230 Constraints with virtual sites to connections,
>> 2596 left
>> Warning: removed 582 Constraints with vsite with Virtual site 3out
>> construction
>> This vsite construction does not guarantee constant bond-length
>> If the constructions were generated by pdb2gmx ignore this
>> warning
>> Cleaning up constraints and constant bonded interactions with virtual
>> sites
>> Removed 1305 Angles with virtual sites, 6251 left
>> Removed 480 Proper Dih.s with virtual sites, 363 left
>> Converted 2230 Constraints with virtual sites to connections,
>> 2596 left
>> Warning: removed 582 Constraints with vsite with Virtual site 3out
>> construction
>> This vsite construction does not guarantee constant bond-length
>> If the constructions were generated by pdb2gmx ignore this
>> warning
>
> According to your experience, this can be pertinent with my problems?
>
Not likely. The virtual sites are within the protein, not the lipids, right?
Without the mdrun output, there's little else I can tell you.
-Justin
> Thank you once again,
>
> Fabio
>
> On 07/27/2011 02:45 PM, Justin A. Lemkul wrote:
>>
>> The problem is indeed as I suspected. Your molecules are broken across
>> periodic boundaries in the initial configuration. When you replicate
>> with genbox, you've now replicated broken molecules such that those at
>> the new interfaces between the boxes appear to be intact, but in fact
>> they are not. This is just an artifact of visualization. If you use
>> "trjconv -pbc whole" on the original starting configuration to make the
>> molecules whole before replicating with genconf -nbox, you will avoid
>> this problem.
>>
>> -Justin
>>
>> Fabio Affinito wrote:
>>> Yes. It's in attachment.
>>>
>>> Fabio
>>>
>>> On 07/27/2011 02:38 PM, Justin A. Lemkul wrote:
>>>>
>>>> Can you please also send me the coordinate file from before you ran
>>>> genconf?
>>>>
>>>> -Justin
>>>>
>>>> Fabio Affinito wrote:
>>>>> Finally, I just got the right compression to fit my file in an
>>>>> attachment.
>>>>> The interesting lines are:
>>>>> 159988 and 159992
>>>>>
>>>>> Kindly regards,
>>>>>
>>>>> Fabio
>>>>>
>>>>> On 07/27/2011 01:42 PM, Justin A. Lemkul wrote:
>>>>>>
>>>>>>
>>>>>> Fabio Affinito wrote:
>>>>>>> On 07/26/2011 07:02 PM, Justin A. Lemkul wrote:
>>>>>>>>
>>>>>>>>
>>>>>>>> Fabio Affinito wrote:
>>>>>>>>> On 07/26/2011 05:06 PM, Justin A. Lemkul wrote:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Fabio Affinito wrote:
>>>>>>>>>>> Maybe this is a different issue... but it's ok that after the
>>>>>>>>>>> 99,999th
>>>>>>>>>>> atom the counter restarts from zero?
>>>>>>>>>>>
>>>>>>>>>>>> 21374SOL OW99999 12.986 9.021 7.036 -0.0037 -0.4345 0.3977
>>>>>>>>>>>> 21374SOL HW1 0 13.069 8.987 7.081 0.5916 0.5409 0.0638
>>>>>>>>>>>
>>>>>>>>>>> Could this be the origin of my problem?
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Atom numbering is not the problem. This happens all the time for
>>>>>>>>>> systems
>>>>>>>>>> of hundreds of thousands of atoms, which Gromacs handles just
>>>>>>>>>> fine.
>>>>>>>>>> Please investigate the points I suggested before.
>>>>>>>>>
>>>>>>>>> Yes, but this doesn't make things easier! :-)
>>>>>>>>> According to the log the atoms to consider are 159986 and 159990
>>>>>>>>>
>>>>>>>>
>>>>>>>> That's not what you posted before. The .log output indicated atoms
>>>>>>>> 193657 and 193660 were problematic.
>>>>>>>
>>>>>>> Sorry. It's because I've tried with many systems (with different
>>>>>>> -nbox
>>>>>>> values) and the error was always the same.
>>>>>>>
>>>>>>>>
>>>>>>>>> Browsing the conf.gro, if I didn't make mistakes this atoms are:
>>>>>>>>>
>>>>>>>>>> 30040POPG OE59986 0.080 13.158 2.964 0.0885 0.4154 -0.0859
>>>>>>>>>
>>>>>>>>>> 30040POPG C1C59990 0.219 26.034 3.221 0.6449 0.0750 0.1313
>>>>>>>>>
>>>>>>>>> But their distance is 12.8nm, while md.log reports 38.911 nm...
>>>>>>>>>
>>>>>>>>
>>>>>>>> In any case, why are atoms four bonds (based on the original .log
>>>>>>>> output
>>>>>>>> of 1-4 interactions being a problem) away separated by 12.8 nm?
>>>>>>>> Seems
>>>>>>>> very odd to me. I ask yet again - what are your box vectors, before
>>>>>>>> and
>>>>>>>> after manipulation with genconf?
>>>>>>>
>>>>>>>
>>>>>>> Seems odd to me, too. For the box vectors (sorry if I didnt answer
>>>>>>> before), in this case:
>>>>>>>
>>>>>>> after: 26.04658 26.04658 8.75317
>>>>>>> before: 13.02329 13.02329 8.75317
>>>>>>>
>>>>>>> Hope it helps.
>>>>>>>
>>>>>>
>>>>>> Without seeing the coordinate files, I can't tell anything
>>>>>> further. If
>>>>>> you want, you can send me (off-list) the coordinate files before and
>>>>>> after genconf and please tell me the exact atoms that are reported as
>>>>>> problematic.
>>>>>>
>>>>>> -Justin
>>>>>>
>>>>>>> Best regards,
>>>>>>>
>>>>>>> Fabio
>>>>>>>
>>>>>>>>
>>>>>>>> -Justin
>>>>>>>>
>>>>>>>>> So what?
>>>>>>>>>
>>>>>>>>> F.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> -Justin
>>>>>>>>>>
>>>>>>>>>>> Thanks again,
>>>>>>>>>>>
>>>>>>>>>>> Fabio
>>>>>>>>>>>
>>>>>>>>>>> On 07/26/2011 04:38 PM, Justin A. Lemkul wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Fabio Affinito wrote:
>>>>>>>>>>>>> On 07/26/2011 04:30 PM, Justin A. Lemkul wrote:
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Fabio Affinito wrote:
>>>>>>>>>>>>>>> On 07/26/2011 04:19 PM, Justin A. Lemkul wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> Were the molecules whole in the coordinate file you
>>>>>>>>>>>>>>>> replicated? If
>>>>>>>>>>>>>>>> not,
>>>>>>>>>>>>>>>> the bonds will now be assigned across the entire box.
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> -Justin
>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> Yes and not, depending on what you mean by "whole".
>>>>>>>>>>>>>>> It is an ion channel, so it's made of four chains.
>>>>>>>>>>>>>>> This clarifies? (i guess not..)
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> By whole, I mean that the molecules are not split across
>>>>>>>>>>>>>> periodic
>>>>>>>>>>>>>> boundaries in the initial configuration that you
>>>>>>>>>>>>>> replicated. If
>>>>>>>>>>>>>> you
>>>>>>>>>>>>>> replicate a periodic break, then you split the molecules by a
>>>>>>>>>>>>>> distance
>>>>>>>>>>>>>> equal to the new periodic distance.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> -Justin
>>>>>>>>>>>>>>
>>>>>>>>>>>>> Ok, so: no, it's not broken.
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> What you need to do is use the information mdrun provided
>>>>>>>>>>>> you to
>>>>>>>>>>>> diagnose what's going on. Apparently atoms 193657 193660 are
>>>>>>>>>>>> separated
>>>>>>>>>>>> by 31 nm. What are your box vectors? Where are these atoms in
>>>>>>>>>>>> the
>>>>>>>>>>>> system? Then you'll have your answer. The only reason I can
>>>>>>>>>>>> think
>>>>>>>>>>>> of for
>>>>>>>>>>>> such extreme distances is a periodicity issue.
>>>>>>>>>>>>
>>>>>>>>>>>> -Justin
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>>
>>
>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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