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Re: [Adun-users] Unable to link system H2OContainer Michael Johnston Thu Feb 02 04:09:32 2012

As I see it this problem is most likely to do with some input options to
the program. The facility to connect the two runs is there and works for me
anyway.

Thus to resolve the problem The question is to determine why it is not
working by either (A) finding the problem with the inputs, or (B)
discovering a bug in Adun. There is no need to implement anything new as of
now.

When we find the problem we may discover that
- We need to improve how to do the link (what was being discussed)
- Provide a more detailed error message
- Fix something in Adun

The message says clearly the number of waters does not match - I've already
explained what could lead to this and how it possibly could be resolved.
Have these suggestions been tried? Is there some reason they can't?

2012/1/19 Jordi Villà i Freixa <[EMAIL PROTECTED]>

> well, this discussion arose because we had a problem connecting
> minimisation with simulation. As I understood from all previous e-mails and
> conversations in the lab, there was a problem to be solved. Now you say
> there is not. Could you guys clarify?
>
> On Jan 19, 2012, at 6:23 PM, Michael Johnston wrote:
>
> What ready? - Everything I mentioned is already done?
>
> 2012/1/19 Jordi Villà i Freixa <[EMAIL PROTECTED]>
>
>> can we have an estimation on when this will be ready, according to
>> everybody's workload?
>>
>>
>> On Jan 19, 2012, at 6:18 PM, Michael Johnston wrote:
>>
>>
>>
>> 2012/1/19 Jordi Villà i Freixa <[EMAIL PROTECTED]>
>>
>>> I am not pretty sure I follow your arguments guys, but here is how I see
>>> it
>>>
>>> -the fact that we have a single datasource file for both topology and
>>> coordinates is problematic, but we can live with that.
>>>
>>> -the only thing that is needed is that after each calculation (call it
>>> minimisation, MD run, or whatever) the program finnishes cleanly by
>>> creating a new datasource with a new name, containing all new coordinates
>>> and velocities (in addition to the topology, of course). That name can be
>>> automatically assigned from Adun if the user does not provide it in the
>>> template. Essentially, as a general rule, a template should contain aways
>>> the names of the files that are used as input plus the names of the files
>>> that will appear as outputs.
>>>
>>> -the difficulty appears to be in reading the datasource that has been
>>> previously produced and use it in a new simulation. That should not be a
>>> problem as the only needed think is to reapply the SCAAS to the new
>>> datasource. Recall the SCAAS affects differently the molecules in the water
>>> container than the moleucles in the protein. For these, there is no such
>>> think as SCAAS but only a constraint if they are lying outside the sphere.
>>> This is the only thing that needs to be fixed right now.
>>>
>>
>> The difficulty is not in what you describe above - there is some
>> trickyness with the water container - but this still can be overcome
>>
>> To summarise, everything you say above is already possible - the linking
>> we discuss just streamlines/automagics the above process for you. It is
>> also more flexible - you don't have to create new input files with
>> coordinates/velocities from just the last frame - you can initialise from
>> any frame in any simulation (of the same protein of course).
>>
>>
>>>
>>> In other words, a datasource contains topology info that should be
>>> considered unmutable (unless we want to discuss reactivity, which is not
>>> the case by now). The coordinates, currently in the datasource, are the
>>> only thing that mutates. Rcall that this differes from other well
>>> established packages where topology and coordinates are in separate files,
>>> but eventually we can live with how adun works right now.
>>>
>>
>> The "initial" coordinates are in the datasource to store all information
>> on a system in one file - so one PDB -> one datasource. This makes many
>> storage and other operations simpler. However you don't have to use the
>> coordinates in the datasource (the linking we discuss) and you can replace
>> the coordinates in it with others. If necessary we can add further ways to
>> set initial coordinates.
>>
>> Also remember the datasource class, and Adun, has been designed to
>> support reactivity from the start - some of the things that are different
>> between it and other packages are because of this.
>>
>>
>>> The SCAAS should be applied automatically to any generated or read
>>> water+protein system, according to the rules above.
>>>
>>> In the medium term, it appears obvious to me to segregate topology from
>>> coordinates in two separate files. This will help a lot in many issues.
>>>
>>> On Jan 19, 2012, at 3:36 PM, Michael Johnston wrote:
>>>
>>> Unfortunately making it automagic essentially is the same as Nils's
>>> suggestion where I had problems previously.
>>>
>>> The only requirement the linking has as it stands is you use the same
>>> input protein datasource for each run (and the same container dimensions of
>>> course) when there is water you also want to link - it seems minimal. The
>>> way I was thinking this would work is that you would just change e.g. the
>>> minimisation template, to remove the minmiser and add the simulator. Then
>>> it will just work.
>>>
>>> I will recheck doing it the way Nils suggested - perhaps the problems
>>> are no more.
>>> One potential issue I see with taking the datasources directly from
>>> another simulation is that you may create a completely different system
>>> then you intended in the template (because you just replace, without
>>> checking, datasources based on names). There would also be a problem in the
>>> case where the topology of the system was being modified in the previous
>>> simulation (and you didn't want the topology modifications).
>>>
>>> If it is possible to do I will add a flag like -ReplaceAll which would
>>> control which method was used.
>>>
>>> 2012/1/19 Jordi Villà i Freixa <[EMAIL PROTECTED]>
>>>
>>>>
>>>> On Jan 19, 2012, at 2:54 PM, Michael Johnston wrote:
>>>>
>>>> > On Thu, Jan 19, 2012 at 11:13 AM, Nils Jan Daniel Drechsel <
>>>> > [EMAIL PROTECTED]> wrote:
>>>> >
>>>> >> Hi Michael,
>>>> >>
>>>> >> one question: Wouldn't it be possible to directly copy the systems
>>>> from
>>>> >> one simulation to the other simulation when the simulations are
>>>> linked and
>>>> >> systems with the same name can be found in the two of them instead of
>>>> >> rebuilding the systems and copying the coordinates and velocities?
>>>> >>
>>>> >
>>>> > This is actually the way I tried first, but there appeared some subtle
>>>> > problem that I can't remember of the top of my head. The way its done
>>>> now
>>>> > was the alternative which I switched to as it had no issues and was
>>>> very
>>>> > quick to implement.
>>>> >
>>>> >
>>>> >> Otherwise I guess there will always be a problem with the water
>>>> container,
>>>> >> since the amount of water molecules depends on the protein volume
>>>> which can
>>>> >> change between simulations.
>>>> >>
>>>> >
>>>> > Yes it can in general, but the linking should use the *same* initial
>>>> > protein configuration as the input to both configurations (in the case
>>>> > where you want to link the container that is) so this shouldn't be an
>>>> issue
>>>> > for it.
>>>> >
>>>> > That is the initial systems built in the first and second runs should
>>>> be
>>>> > identical as far as the number of solvent molecules goes. Then all
>>>> you do
>>>> > is change the initial coordinates/velocities of the second run to
>>>> those in
>>>> > frame X of the first run to start from that point.
>>>>
>>>> that seems like an excellent solution and not at all unelegant.
>>>> However, this should be done automagically in the program (regarding your
>>>> next sentence). Can this be set up?
>>>>
>>>> >
>>>> > Perhaps this is the problem - is the simulation being started from
>>>> the same
>>>> > conditions as the minimisation?
>>>> >
>>>> >
>>>> >>
>>>> >> On Thu, Jan 19, 2012 at 10:23 AM, Michael Johnston <
>>>> >> [EMAIL PROTECTED]> wrote:
>>>> >>
>>>> >>> This is the same error as previous -
>>>> >>>
>>>> >>> 2012-01-18 20:13:46.958 AdunCore[7501] Error code 13
>>>> >>>> 2012-01-18 20:13:46.958 AdunCore[7501] Description - Unable to set
>>>> >>>> coordinates for H2OContainer using link
>>>> >>>> *2012-01-18 20:13:46.958 AdunCore[7501] Detail - The two systems
>>>> do not
>>>> >>>> **contain the same number of elements*
>>>> >>>
>>>> >>>
>>>> >>>
>>>> >>> Check the entry for HOH-Container in the Minimisation log and this
>>>> log
>>>> >>> for
>>>> >>> descrepencies
>>>> >>>
>>>> >>> On Wed, Jan 18, 2012 at 7:36 PM, deepak kumar <
>>>> [EMAIL PROTECTED]
>>>> >>>> wrote:
>>>> >>>
>>>> >>>> I tried to run the simulation. Minimization went fine, but got this
>>>> >>> error.
>>>> >>>>
>>>> >>>>
>>>> >>>> AdunCore.log file looks like this :
>>>> >>>>
>>>> >>>> Linking from simulation at
>>>> SimulationOutput/Minimisation1.simulation
>>>> >>>>       No trajectory specified - defaulting to active
>>>> >>>>       This is at
>>>> >>>>
>>>> >>>>
>>>> >>>
>>>> file:/cbbl/users/deepak/simulations/mac_2kxn_with_RNA_maestro_without_minimization/SimulationOutput/Minimisation1.simulation/Trajectory0/
>>>> >>>>       Systems to link not specified - defaulting to all:
>>>> H2OContainer,
>>>> >>>> 2kxnB_maestroreduce_xleap_fixed
>>>> >>>>       Linking to last checkpoint (1001)
>>>> >>>>       Linked coordinates of system 2kxnB_maestroreduce_xleap_fixed
>>>> >>>>       Linked velocities of system 2kxnB_maestroreduce_xleap_fixed
>>>> >>>>       Unable to link system H2OContainer. See error log.
>>>> >>>>
>>>> >>>> AdunCore.errors file looks like this :
>>>> >>>>
>>>> >>>> 2012-01-18 20:13:44.581 AdunCore[7501] Force field Amber99SB
>>>> >>>> 2012-01-18 20:13:44.717 AdunCore[7501] Force field Amber99SB
>>>> >>>> 2012-01-18 20:13:44.940 AdunCore[7501] Force field GAFF
>>>> >>>> 2012-01-18 20:13:45.343 AdunCore[7501] Stored URL is
>>>> >>>>
>>>> >>>>
>>>> >>>
>>>> file://localhost/cbbl/users/deepak/simulations/mac_2kxn_with_RNA_maestro_without_minimization/SimulationOutput/Minimisation1.simulation/
>>>> >>>> GSCBufferString
>>>> >>>> 2012-01-18 20:13:45.343 AdunCore[7501] Decode data URL
>>>> >>>>
>>>> >>>>
>>>> >>>
>>>> file://localhost/cbbl/users/deepak/simulations/mac_2kxn_with_RNA_maestro_without_minimization/SimulationOutput/Minimisation1.simulation/
>>>> >>>> and path
>>>> >>>>
>>>> >>>>
>>>> >>>
>>>> /cbbl/users/deepak/simulations/mac_2kxn_with_RNA_maestro_without_minimization/SimulationOutput/Minimisation1.simulation/
>>>> >>>> 2012-01-18 20:13:46.719 AdunCore[7501] Replaced coordinates of
>>>> system
>>>> >>>> 2kxnB_maestroreduce_xleap_fixed with those from link
>>>> >>>> 2012-01-18 20:13:46.726 AdunCore[7501] Replaced velocties of
>>>> system
>>>> >>>> 2kxnB_maestroreduce_xleap_fixed with those from link
>>>> >>>> 2012-01-18 20:13:46.957 AdunCore[7501] Unable to set coordinates
>>>> for
>>>> >>>> H2OContainer using link
>>>> >>>> 2012-01-18 20:13:46.957 AdunCore[7501] Incompatible number of
>>>> elements
>>>> >>>> 2012-01-18 20:13:46.958 AdunCore[7501] Detected error at top
>>>> level -
>>>> >>>> Simulation exiting
>>>> >>>> 2012-01-18 20:13:46.958 AdunCore[7501] Error details follow
>>>> >>>> 2012-01-18 20:13:46.958 AdunCore[7501] Logging error from domain
>>>> >>>> AdunCore.ErrorDomain
>>>> >>>> 2012-01-18 20:13:46.958 AdunCore[7501] Error code 13
>>>> >>>> 2012-01-18 20:13:46.958 AdunCore[7501] Description - Unable to set
>>>> >>>> coordinates for H2OContainer using link
>>>> >>>> 2012-01-18 20:13:46.958 AdunCore[7501] Detail - The two systems
>>>> do not
>>>> >>>> contain the same number of elements
>>>> >>>> Processing link {simulation =
>>>> >>> SimulationOutput/Minimisation1.simulation; }
>>>> >>>> ~
>>>> >>>>
>>>> >>>> ~
>>>> >>>>
>>>> >>>> ~
>>>> >>>>
>>>> >>>>
>>>> >>>>
>>>> >>>> --
>>>> >>>> Deepak Kumar
>>>> >>>>
>>>> >>>> This message has been automatically forwarded to you by the Adun
>>>> team
>>>> >>>> http://adun.imim.es
>>>> >>>> _______________________________________________
>>>> >>>> Adun-users mailing list
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>>>> >>>> https://mail.gna.org/listinfo/adun-users
>>>> >>>>
>>>> >>>
>>>> >>> This message has been automatically forwarded to you by the Adun
>>>> team
>>>> >>> http://adun.imim.es
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>>>> >>
>>>> >>
>>>> >
>>>> > This message has been automatically forwarded to you by the Adun team
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>>>> > _______________________________________________
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>>>>
>>>> --
>>>> Jordi Villà i Freixa
>>>> Computational Biochemistry and Biophysics lab
>>>> Research Group on Biomedical Informatics (GRIB) - IMIM/UPF
>>>> Parc de Recerca Biomèdica de Barcelona
>>>> C/ Doctor Aiguader, 88; 08003 Barcelona (Spain)
>>>> Tel: +34 93 316 0504 // Fax: +34 93 316 0550
>>>> e-mail: [EMAIL PROTECTED]
>>>> http://cbbl.imim.es
>>>>
>>>>
>>>
>>>   --
>>> Jordi Villà i Freixa
>>> Computational Biochemistry and Biophysics lab
>>> Research Group on Biomedical Informatics (GRIB) - IMIM/UPF
>>> Parc de Recerca Biomèdica de Barcelona
>>> C/ Doctor Aiguader, 88; 08003 Barcelona (Spain)
>>> Tel: +34 93 316 0504 // Fax: +34 93 316 0550
>>> e-mail: [EMAIL PROTECTED]
>>> http://cbbl.imim.es
>>>
>>>
>>
>>   --
>> Jordi Villà i Freixa
>> Computational Biochemistry and Biophysics lab
>> Research Group on Biomedical Informatics (GRIB) - IMIM/UPF
>> Parc de Recerca Biomèdica de Barcelona
>> C/ Doctor Aiguader, 88; 08003 Barcelona (Spain)
>> Tel: +34 93 316 0504 // Fax: +34 93 316 0550
>> e-mail: [EMAIL PROTECTED]
>> http://cbbl.imim.es
>>
>>
>
> --
> Jordi Villà i Freixa
> Computational Biochemistry and Biophysics lab
> Research Group on Biomedical Informatics (GRIB) - IMIM/UPF
> Parc de Recerca Biomèdica de Barcelona
> C/ Doctor Aiguader, 88; 08003 Barcelona (Spain)
> Tel: +34 93 316 0504 // Fax: +34 93 316 0550
> e-mail: [EMAIL PROTECTED]
> http://cbbl.imim.es
>
>

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