Re: [gmx-users] Tpr version check

[Erik Marklund]

Hi,

Thanks Mark. See https://redmine.gromacs.org/issues/2924.

Kind regards,
Erik
__
Erik Marklund, PhD, Associate Professor of Biochemistry
Associate Senior Lecturer in Computational Biochemistry
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4562
erik.markl...@kemi.uu.se

On 11 Apr 2019, at 08:42, Mark Abraham 
mailto:mark.j.abra...@gmail.com>> wrote:

Hi,

The old behavior of a graceful rejection of the file with a new version
number is still expected.

The most likely explanation for your observations is that they old version
of gmx is linking somehow to newer versions of things (which also shouldn't
happen ...), and the chimera can't work.
If you can share a tpr on Redmine we can see if there is an issue we can
fix.

Mark

On Wed., 10 Apr. 2019, 23:05 Erik Marklund, 
mailto:erik.markl...@kemi.uu.se>>
wrote:

Hi users,

I accidentally used an older version (2016.3) to run trjconv on some
trajectories. Some conversions worked, seemingly depending on pbc options
etc, whereas others stopped with the following output:

Back Off! I just backed up mol.xtc to ./#mol.xtc.1#
->  frame  0 time0.000
---
Program: gmx trjconv, version 2016.3
Source file: src/gromacs/pbcutil/pbc.cpp (line 94)

Fatal error:
Unknown ePBC=1051770189 in ePBC2npbcdim

Call me a hopeless nostalgic, but I remember a time when such mistakes
rendered an error saying that I am using an older version of gmx than the
version used to generate the tpr file. Is that not a thing anymore, and
this is the expected behaviour? Seems problematic if gmx tools try to read
nonsense data (from the viewpoint of the gromacs version used).

Kind regards,
Erik
__
Erik Marklund, PhD, Associate Professor of Biochemistry
Associate Senior Lecturer in Computational Biochemistry
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4562
erik.markl...@kemi.uu.se









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Re: [gmx-users] Tpr version check

[Mark Abraham]

Hi,

The old behavior of a graceful rejection of the file with a new version
number is still expected.

The most likely explanation for your observations is that they old version
of gmx is linking somehow to newer versions of things (which also shouldn't
happen ...), and the chimera can't work.
If you can share a tpr on Redmine we can see if there is an issue we can
fix.

Mark

On Wed., 10 Apr. 2019, 23:05 Erik Marklund, 
wrote:

> Hi users,
>
> I accidentally used an older version (2016.3) to run trjconv on some
> trajectories. Some conversions worked, seemingly depending on pbc options
> etc, whereas others stopped with the following output:
>
> Back Off! I just backed up mol.xtc to ./#mol.xtc.1#
>  ->  frame  0 time0.000
> ---
> Program: gmx trjconv, version 2016.3
> Source file: src/gromacs/pbcutil/pbc.cpp (line 94)
>
> Fatal error:
> Unknown ePBC=1051770189 in ePBC2npbcdim
>
> Call me a hopeless nostalgic, but I remember a time when such mistakes
> rendered an error saying that I am using an older version of gmx than the
> version used to generate the tpr file. Is that not a thing anymore, and
> this is the expected behaviour? Seems problematic if gmx tools try to read
> nonsense data (from the viewpoint of the gromacs version used).
>
> Kind regards,
> Erik
> __
> Erik Marklund, PhD, Associate Professor of Biochemistry
> Associate Senior Lecturer in Computational Biochemistry
> Department of Chemistry – BMC, Uppsala University
> +46 (0)18 471 4562
> erik.markl...@kemi.uu.se
>
>
>
>
>
>
>
>
>
> När du har kontakt med oss på Uppsala universitet med e-post så innebär
> det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör
> det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
>
> E-mailing Uppsala University means that we will process your personal
> data. For more information on how this is performed, please read here:
> http://www.uu.se/en/about-uu/data-protection-policy
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
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[gmx-users] Tpr version check

[Erik Marklund]

Hi users,

I accidentally used an older version (2016.3) to run trjconv on some 
trajectories. Some conversions worked, seemingly depending on pbc options etc, 
whereas others stopped with the following output:

Back Off! I just backed up mol.xtc to ./#mol.xtc.1#
 ->  frame  0 time0.000
---
Program: gmx trjconv, version 2016.3
Source file: src/gromacs/pbcutil/pbc.cpp (line 94)

Fatal error:
Unknown ePBC=1051770189 in ePBC2npbcdim

Call me a hopeless nostalgic, but I remember a time when such mistakes rendered 
an error saying that I am using an older version of gmx than the version used 
to generate the tpr file. Is that not a thing anymore, and this is the expected 
behaviour? Seems problematic if gmx tools try to read nonsense data (from the 
viewpoint of the gromacs version used).

Kind regards,
Erik
__
Erik Marklund, PhD, Associate Professor of Biochemistry
Associate Senior Lecturer in Computational Biochemistry
Department of Chemistry – BMC, Uppsala University
+46 (0)18 471 4562
erik.markl...@kemi.uu.se









När du har kontakt med oss på Uppsala universitet med e-post så innebär det att 
vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du 
läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/

E-mailing Uppsala University means that we will process your personal data. For 
more information on how this is performed, please read here: 
http://www.uu.se/en/about-uu/data-protection-policy
-- 
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