[gmx-users] QM / MM assistance

[Eric Smoll]

Hello Justin,

Thank you for the input. I switched to ORCA and it was much easier going. I
used the following cmake command.

TMP=$(echo
/opt/apps/intel/13/composer_xe_2013.2.146/mkl/lib/intel64/libmkl* | tr ' '
':')
cmake -DCMAKE_PREFIX_PATH="/a/b/c/QMMM/fftw/3.3.4" \
-DCMAKE_INSTALL_PREFIX=/a/b/c/QMMM/gromacs/4.6.7/serial -DGMX_X11=OFF \
-DCMAKE_CXX_COMPILER=icpc -DCMAKE_C_COMPILER=icc
-DGMX_PREFER_STATIC_LIBS=ON -DGMX_MPI=OFF \
-DGMX_QMMM_PROGRAM=ORCA -DGMX_DOUBLE=ON ../gromacs-4.6.7 \
-DGMX_FFT_LIBRARY=mkl -DMKL_LIBRARIES="$TMP" \
-DMKL_INCLUDE_DIR="/opt/apps/intel/13/composer_xe_2013.2.146/mkl/include"

This compiles nicely with no errors on the machine I am using. Thank you
for the guidance.

Best,
Eric

On Sun, Sep 14, 2014 at 11:14 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/14/14 12:59 PM, Eric Smoll wrote:
>
>> Hello Johnny,
>>
>> Thanks for the suggestion. I dumped the contents of CMakeError.log below.
>> I
>> am not sure why the C compiler failed. The error occurs on directory
>> change? Later in the log, libmopac.a fails. Is this a static/shared
>> problem?
>>
>>
> What is your full cmake command?  Do you have to do anything special to
> configure your environment (module loading, etc)?
>
>  This page (http://wwwuser.gwdg.de/~ggroenh/qmmm.html) contains the
>> following instructions. "Compile all mopac files (f77 -O2 -c *.f), except
>> mopac.f, moldat.f and deriv.f (thes ones are to be replaced by gmxmop.f),
>> and collect the objects (*.o) into a library (ar rcv libmopac.a *.o;ranlib
>> libmopac.a). Or if you are using linux, simply download libmopac.a
>> instead." libmopac.a is not working for me. mopac.f is not
>> in mopac7-1.11/fortran. Should I ignore its absence or
>> replace mopac7app.f and mopac7lib.f instead?
>>
>>
> The main problem here is you're trying to follow instructions designed for
> 10-year-old software on the current version.  I would expect it to fail.
> The QM/MM interface is largely unmaintained.  It has been slated for a
> complete re-write for years, but it hasn't been finished.  ORCA should
> compile (I fixed a few random bugs related to that a while back), but
> beyond that, I have no idea.  FWIW, I tried Mopac years ago and it never
> worked.  That was in the 4.0.x series.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
>
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