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Re: [Adun-users] Unable to link system H2OContainer Jordi Villà i Freixa Thu Feb 02 04:07:13 2012

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
>>>> 
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>>>> http://adun.imim.es
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>>>> 
>>> 
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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



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