OK, I got fort.7 to be written now, when using g09.
There was an issue with my environment setup, which caused executing "g09 "
on the command-line to actually run g03 (/share/apps//g03/l1.exe).
After solving that, it turned out that when I ran g09 (properly), fort.7
was written.
So *I think* this issue is solved now.
My question about a 'true' single-point QM/MM energy calculation still
stands, though. But this may be difficult with the current sander-code, as
I think people typically do a minimization with maxcyc=1 to get
single-point energies. In this case, one would be calculating gradients as
well, of course.
Thanks,
Marc
On 15 May 2012 09:36, Marc van der Kamp <marcvanderkamp.gmail.com> wrote:
> 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 - 02:30:03 PDT
