Re: [Adun-users] Unable to link system H2OContainer

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
>>> >>>> _______________________________________________
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>>> >>>> https://mail.gna.org/listinfo/adun-users
>>> >>>>
>>> >>>
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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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