<< Drying the trayectories >>

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I. Camps

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Jun 4, 2022, 2:39:29 PMJun 4
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Hello,

I was using the code below to get the dried trajectories with MDAnalysis v2.1dev:

complexx_temp = u2.select_atoms(sel_prot, sel_lig)
# New Universe just with protein+ligand (dry)
u = mda.Merge(complexx_temp).load_new(
         AnalysisFromFunction(lambda ag: ag.positions.copy(),
                              complexx_temp).run().results,
         format=MemoryReader)

After upgrading my Ubuntu, my conda MDAnalysis enviroment stop working (even after deleting/removing/re-installing), so I installed MDAnalysis directly on my system using pip (now I have v2.2).

With the new version, I am not able to run the code above, returning some errors.

I appreciate any help!

Screenshot from 2022-06-04 15-38-00.png
Regards,

Camps

Oliver Beckstein

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Jun 6, 2022, 1:31:01 PMJun 6
to mdnalysis-discussion
Hi,

I am not quite sure why the MemoryReader transfer would have broken between releases. Are you able to reproduce the issue with some of our test trajectories such as

from MDAnalysisTests import datafiles as data
u = mda.Universe(data.TPR, data.XTC)


Also, did you check if you can provide the order=“f” kwarg to the Universe… I am sorry I don’t have time to check the docs or try it.

Oliver

<Screenshot from 2022-06-04 15-38-00.png>
Regards,

Camps

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I. Camps

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Jun 8, 2022, 10:11:15 AMJun 8
to MDnalysis discussion
Hello Oliver,

Using the test data I got the same errors.

I don't have a clue about how to provide the order=“f” kwarg to the Universe, sorry for that ;(

Oliver Beckstein

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Jun 8, 2022, 1:49:35 PMJun 8
to mdnalysis-discussion
Hi,

On Jun 8, 2022, at 7:11 AM, I. Camps <ica...@gmail.com> wrote:

Hello Oliver,

Using the test data I got the same errors.

Ok, then that looks like a bug.

Could you please raise an issue at https://github.com/MDAnalysis/mdanalysis/issues ? You’ll get a template to fill in. Th closer you follow the instructions, the easier it will be for someone to address the problem. 

In particular, paste the code with the example files that leads to the failure. Also past the output that demonstrates the failure. Once we can reproduce a problem, it gets a lot easier to fix.

Thanks,
Oliver


I don't have a clue about how to  provide the order=“f” kwarg to the Universe, sorry for that ;(

On Monday, June 6, 2022 at 2:31:01 PM UTC-3 orbe...@mdanalysis.org wrote:
Hi,

I am not quite sure why the MemoryReader transfer would have broken between releases. Are you able to reproduce the issue with some of our test trajectories such as

from MDAnalysisTests import datafiles as data
u = mda.Universe(data.TPR, data.XTC)


Also, did you check if you can provide the order=“f” kwarg to the Universe… I am sorry I don’t have time to check the docs or try it.

Oliver

On Jun 4, 2022, at 11:39 AM, I. Camps <ica...@gmail.com> wrote:

Hello,

I was using the code below to get the dried trajectories with MDAnalysis v2.1dev:

complexx_temp = u2.select_atoms(sel_prot, sel_lig)
# New Universe just with protein+ligand (dry)
u = mda.Merge(complexx_temp).load_new(
         AnalysisFromFunction(lambda ag: ag.positions.copy(),
                              complexx_temp).run().results,
         format=MemoryReader)

After upgrading my Ubuntu, my conda MDAnalysis enviroment stop working (even after deleting/removing/re-installing), so I installed MDAnalysis directly on my system using pip (now I have v2.2).

With the new version, I am not able to run the code above, returning some errors. 

I appreciate any help!

<Screenshot from 2022-06-04 15-38-00.png>
Regards,

Camps


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I. Camps

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Jun 24, 2022, 8:31:28 AMJun 24
to MDnalysis discussion
UPDATE:

Changing results to results.timeseries fixes the problem!

Oliver Beckstein

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Jun 24, 2022, 12:40:15 PMJun 24
to mdnalysis-discussion
Thank you for adding the solution here, that’s very useful for posterity. I am glad it wasn’t a bug.

(Also thank you for Jonathan for providing the answer at https://github.com/MDAnalysis/mdanalysis/issues/3732.)

Oliver

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