Hi again,
Thanks for the reply.
I ran gaussian (g03 and g09) with the gau_job.inp input file in
$AMBERHOME/test/qmmm_EXTERN/pure_QM_MD_GAUSSIAN
The only files that are created are gau_job.log and gau_job.chk, with
gau_job.log terminating normally.
fort.7 is not created.
Should the gau_job.log say anything about dumping the gradients?
In my standard environment, GAUSS_SCRDIR=/tmp
I changed this to the working directory
($AMBERHOME//test/qmmm_EXTERN/pure_QM_MD_GAUSSIAN), in case the fort.7 file
would be written to GAUSS_SCRDIR, but this didn't make a difference.
I've also verified with our sysadmin that our g03 and g09 binaries are
standard binaries.
Any further thoughts on what may be happening / how to fix this?
As a side-question: would it be possible to do a true single-point energy
calculation with AMBER/Gaussian, i.e. without needing to get the gradients?
If so, how?
Thanks,
Marc
On 14 May 2012 20:52, Andreas Goetz <agoetz.sdsc.edu> wrote:
> I have relied on Gaussian's manual when implementing this:
> http://www.gaussian.com/g_tech/g_ur/k_punch.htm
>
> The input file that the interface to Gaussian creates (gau_job.inp)
> contains "Punch=Derivatives" in the route section. According to Gaussian
> this should dump gradients to fort.7. Can you run Gaussian with this input
> file and check any files that are created? Are you aware of any
> modifications during the Gaussian installation?
>
> All the best,
> Andy
>
> PS: I am on travel this week and might not respond immediately to email.
>
> On May 14, 2012, at 12:41 PM, Jason Swails wrote:
>
> > So what is happening here is that fort.7 is not being written but sander
> expects it there.
> >
> > The implementors will have to look into this now, but any info you can
> give to help them reproduce the issue would probably help them.
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> >
> > On May 14, 2012, at 9:39 AM, Marc van der Kamp <marcvanderkamp.gmail.com>
> wrote:
> >
> >> Hi Jason,
> >>
> >> Thanks for the reply - I made the change and recompiled.
> >> I don't get an error message about fort.7 not existing, but the job
> stops
> >> (abruptly) after writing:
> >>
> --------------------------------------------------------------------------------
> >> 4. RESULTS
> >>
> --------------------------------------------------------------------------------
> >>
> >> Again, gau_job.log is present and shows that Gaussian
> >> has successfully finished.
> >> The fort.7 file is not present this time (which makes sense), but the
> >> underlying problem still persists, it appears.
> >> Again, this is the case for tests in:
> >> AMBERHOME/test/qmmm_EXTERN/QMMM_MD_GAUSSIAN
> >> AMBERHOME/test/qmmm_EXTERN/pure_QM_MD_GAUSSIAN/
> >>
> >> Thanks,
> >> Marc
> >>
> >>
> >> On 14 May 2012 14:12, Jason Swails <jason.swails.gmail.com> wrote:
> >>
> >>> The problem seems to be that the Amber/Gaussian interface depends on
> all of
> >>> the gradient information being dumped to the file "fort.7", which it
> claims
> >>> will always exist. However, I'm skeptical that this is always true.
> >>>
> >>> Can you modify the source code and change line 600 of the file
> >>> qm2_extern_gau_module.F90 (in $AMBERHOME/src/sander) from
> >>>
> >>> open(iunit, file=fortfile) !Will always exist
> >>>
> >>> to
> >>>
> >>> open(iunit, file=fortfile, status='old') !Will always exist
> >>>
> >>> This way, if the file doesn't exist, it will bomb out rather than
> create
> >>> the file and then immediately fail to parse it. (Really, I think all
> of
> >>> the file opening in the external module should use the amopen() wrapper
> >>> rather than calling "open" directly, since it standardizes most of this
> >>> behavior).
> >>>
> >>> After you do this (and recompile), do you get an error message about
> fort.7
> >>> not existing?
> >>>
> >>> Thanks!
> >>> Jason
> >>>
> >>> On Mon, May 14, 2012 at 12:58 AM, Marc van der Kamp <
> >>> marcvanderkamp.gmail.com> wrote:
> >>>
> >>>> Dear all,
> >>>>
> >>>> I have installed AMBER12 a little while ago, with gnu compilers gcc
> 4.1.2
> >>>> and gfortran 4.1.2 (on a cluster running Rocks 5.3, equivalent to Red
> Hat
> >>>> 4.1.2-50).
> >>>>
> >>>> I would like to try out AMBER/Gaussian, and we have g09 as well as
> g03.
> >>>> I run into problems when running the tests in
> >>>> $AMBERHOME/test/qmmm_EXTERN/QMMM_MD_GAUSSIAN.
> >>>> According to the mdout, Gaussian is found (in this case g09), but
> sander
> >>>> fails with the following:
> >>>>
> >>>> SANDER BOMB in subroutine read_results (qm2_extern_gau_module)
> >>>> Error reading file fort.7
> >>>> Will quit now
> >>>>
> >>>> gau_job.log is present and shows that Gaussian has successfully
> finished.
> >>>> The fort.7 file in the directory is empty, so it is not a surprise
> that
> >>> the
> >>>> job fails.
> >>>> But I don't know how to proceed to fix this. Any help is appreciated!
> >>>>
> >>>> BTW, the same error occurs when using g03 and in the
> pure_QM_MD_GAUSSIAN/
> >>>> tests.
> >>>>
> >>>> Many thanks,
> >>>> Marc
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>
> >>>
> >>>
> >>> --
> >>> Jason M. Swails
> >>> Quantum Theory Project,
> >>> University of Florida
> >>> Ph.D. Candidate
> >>> 352-392-4032
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Dr. Andreas W. Goetz
> Assistant Project Scientist
> San Diego Supercomputer Center
> Tel : +1-858-822-4771
> Email: agoetz.sdsc.edu
> Web : www.awgoetz.de
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue May 15 2012 - 02:00:04 PDT
