Hi,
I can't reproduce your issue. Would you mind sending me some files
off-list that I can use to reproduce the problem? Thanks!
-Dan
On Wed, Sep 28, 2016 at 2:48 AM, Filip Persson <filip.persson.bpc.lu.se> wrote:
> 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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>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> 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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--
-------------------------
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 - 07:00:02 PDT
