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Re: [Adun-users] Unable to link system H2OContainer Nils Jan Daniel Drechsel Thu Feb 02 04:06:43 2012

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?
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.

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
> > [EMAIL PROTECTED]
> > https://mail.gna.org/listinfo/adun-users
> >
>
> This message has been automatically forwarded to you by the Adun team
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