Putting all actions - ie. trajin, autoimage and trajout - in the input file instead does not resolve the issue. Again, specifying the .nc extension for the trajout file gives the correct imaging.
I am not affected by this bug since I only use netcdf format anyway, but it is an odd issue nevertheless.
/Filip
________________________________________
Från: Daniel Roe <daniel.r.roe.gmail.com>
Skickat: den 19 september 2016 16:20
Till: AMBER Mailing List
Ämne: Re: [AMBER] autoimage bug?
Does the issue happen if you put the trajectory output in the script
(i.e. use 'trajout $currFile') instead of on the command line?
-Dan
On Thu, Sep 8, 2016 at 8:32 AM, Filip Persson <filip.persson.bpc.lu.se> wrote:
> Hi Dan!
> So I call cpptraj in a bash script as
>
> cpptraj -p ${prmFile[0]} -i autoimage.cpptraj -y $ifileName -x $currFile
>
> where autoimage.cpptraj is the input file containing only the action
> "autoimage", $ifileName points to an input trajectory file in
> .mdcrd-format and $currFile is the name of the new trajectory file from
> trajout with extension .mdcrd or .nc.
>
> When I put the .mdcrd extension for my trajout file my protein is
> stretched over different periodic images. But when I use the .nc
> extension for the outfile my system is propertly imaged and centered.
>
> My version of cpptraj is V.15.00
>
> Best,
> Filip
>
>
> On 2016-08-31 15:22, Daniel Roe wrote:
>> The output format should have no effect on any actions whatsoever. I cannot
>> reproduce this behavior. Could you send the exact cpptraj input you are
>> using, as well as the version?
>>
>> -Dan
>>
>> On Monday, August 29, 2016, Filip Persson <filip.persson.bpc.lu.se> wrote:
>>
>>> Dear Amber users!
>>> I noticed that the autoimage routine in cpptraj produce inconsistent
>>> results depening on the trajout file format; when writing output in the
>>> (binary) trajectory format netcdf (.nc) I get the correct centering and
>>> imaging of my system, but not when using the Amber trajectory format
>>> (.crd). My input files are in default (.crd) Amber trajectory file
>>> format. Is this a bug in cpptraj?
>>>
>>>
>>> Best regards,
>>> Filip
>>>
>>>
>>> Filip Persson, PhD student
>>> Biophysical Chemistry
>>> Lund University, Sweden
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org <javascript:;>
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>
> --
>
>
> logo *Filip Persson * <mailto:filip.persson.bpc.lu.se> • PhD student
> <http://www.cmps.lu.se/bpc/people/filip-persson/>
> Biophysical Chemistry <http://www.cmps.lu.se/bpc/> • Lund University
> <https://www.google.se/maps/place/Kemicentrum,+223+62+Lund/.55.7153178,13.2087657,17z/data=%214m2%213m1%211s0x46539634d3eb8045:0xab6374345b1b461e>
>
>
>
>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Wed Sep 28 2016 - 00:00:02 PDT
