Hi,
This bug is the result of the second vector not being explicitly
initialized in ptraj, so the behavior becomes compiler-dependent. Note
that this functionality has been implemented and fixed in cpptraj, so
you should not see this issue with cpptraj.
-Dan
On Thu, Jun 7, 2012 at 5:23 AM, Benjamin Stauch <ben.ebi.ac.uk> wrote:
> Dear all,
>
> having recently installed the latest versions of AmberTools12, including
> all auto-updates as of June 6th 2012, locally on a Mac and on our linux
> farm I discovered ptraj behaves differently on both systems when trying
> to compute a time auto-correlation function:
>
> on my Mac, the following script would run through generating the
> expected output,
>
> > ptraj my.psf my.script
>
> with my.script as
>
> trajin my.dcd
> vector v0 .1 corr .2 order 2
> analyze timecorr vec1 v0 tstep 1.0 tcorr 1000.0 out my.out
>
>
> while under linux it failed with the following and at that time cryptic
> warning,
>
> WARNING in ptraj(), analyze timecorr: different attributes for vec1 and
> vec2, ignoring command
>
>
> obviously, this caused me some major headache since the input files were
> 100% identical, and also the ptraj versions the same, freshly compiled
> (Version: "AMBER 12.0 integrated" (4/2012)).
>
> Luckily the advise given at http://archive.ambermd.org/201107/0355.html
> was hinting at how to fix the problem: the linux version was expecting a
> "cross-correlation" kind of definition of the auto-correlation I wanted
> to compute,
>
> analyze timecorr vec1 v0 vec2 v0 tstep 1.0 tcorr 25000.0 dplr out my.out
>
> instead of
>
> analyze timecorr vec1 v0 tstep 1.0 tcorr 25000.0 dplr out my.out
>
> gave me the desired output, while the Mac version seemed to be less
> picky about the syntax.
> This looks a bit suspicious to me ... so I hope this report might be of
> value to some.
>
>
>
>
> cheers
> Ben
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Lab Specialist
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Thu Jun 07 2012 - 06:30:03 PDT
