[gmx-users] Failed to find GROMACS magic number in trr frame header

[Mijiddorj B]

Dear Justin,

Thank you very much for your reply. I see. I cut trr file several ns before
the stopped frame, and I would like to cut the corresponding checkpoint
file before the stopped frame.
Is it possible to get the specific frame checkpoint using gmx?
I would like to re-perform the extended simulation again starting from
another frame. Is it also possible to use the original checkpoint file as
it is?

Best regards,
Mijiddorj


----------------------------
>
> Message: 5
> Date: Sun, 19 Apr 2020 15:36:11 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Failed to find GROMACS magic number in trr
>         frame header
> Message-ID: <b17da565-8a87-ffbf-42ce-bf3958c28e55 at vt.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
>
>
> On 4/18/20 5:38 AM, Mijiddorj B wrote:
> > Dear Justin,
> >
> > Thank you very much for your reply. I see. However, I have one more
> > question. Is it caused by usage of -noappend or other reasons?
>
> No, it's because of the power failure likely causing an issue on the
> filesystem or with your file directly.
>
> -Justin
>
> > Best regards,
> >
> > Mijiddorj
> >
> > ---------------------------------------------------------
> >> Message: 1
> >> Date: Fri, 17 Apr 2020 11:51:25 -0400
> >> From: Justin Lemkul <jalemkul at vt.edu>
> >> To: gmx-users at gromacs.org
> >> Subject: Re: [gmx-users] Failed to find GROMACS magic number in trr
> >>          frame header
> >> Message-ID: <77b40330-739a-c03e-85f2-1bc74b97cb65 at vt.edu>
> >> Content-Type: text/plain; charset=utf-8; format=flowed
> >>
> >>
> >>
> >> On 4/17/20 10:13 AM, Mijiddorj B wrote:
> >>> Dear GMX users,
> >>>
> >>> Hello, I performed MD simulation using gromacs 2018.7v. During this
> >>> simulation, the calculation was stopped because of the electric cut.
> >> Then,
> >>> I continued the simulation using "gmx mdrun with -noappend" in order to
> >> get
> >>> separate trajectory for the safety of data. After that, I would like to
> >>> concatenate the trr files.
> >>> However, I received following error message.
> >>>
> >>> How, can I concatenate these trajectories.
> >>> **********************************************
> >>> Program:     gmx trjcat, version 2018.7
> >>> Source file: src/gromacs/fileio/trrio.cpp (line 114)
> >>>
> >>> Fatal error:
> >>> Failed to find GROMACS magic number in trr frame header, so this is
> not a
> >>> trr
> >>> file!
> >>>
> >>> For more information and tips for troubleshooting, please check the
> >> GROMACS
> >>> website at http://www.gromacs.org/Documentation/Errors
> >>> ************************************************
> >> Your file is corrupted and you will have to run that portion of the
> >> simulation again.
> >>
> >> -Justin
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Assistant Professor
> >> Office: 301 Fralin Hall
> >> Lab: 303 Engel Hall
> >>
> >> Virginia Tech Department of Biochemistry
> >> 340 West Campus Dr.
> >> Blacksburg, VA 24061
> >>
> >> jalemkul at vt.edu | (540) 231-3129
> >> http://www.thelemkullab.com
> >>
> >> ==================================================
> >>
> >>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
>
>
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>
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> End of gromacs.org_gmx-users Digest, Vol 192, Issue 71
> ******************************************************
>