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
>>
>>
>>
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>> 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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Received on Thu Sep 08 2016 - 06:00:02 PDT
