[gmx-users] Re: QMMM cpmd

[Christian Seifert]

Hi Stefan,

Orca is quite ok (but scalability is not comparable with CPMD). Two mpi
versions should be no problem. I have several mpis running here...

@all: Is there an Orca support in 4.0.7 or do one has to use some latest
git stuff?

I never tried semi-empiric (mopac) and as far a I know the other QM
programs do not scale that good.

Greets,
Christian

On Tue, 2010-06-01 at 11:02 -0300, stefhoor wrote:
> Hi Christian, that's a pity, isn't it? I don't think I will use this
> ancient version of gromacs. It is actually quite hard to use QM/MM
> with gromacs, I've tried to compile with mopac, and failed. I still
> don't know what the problem is. Gerrit answered my email saying u
> should link everything with g2c and I still don't have a clue what he
> meant with that. Gamess-UK is paid, and I am not willing to pay for
> something if I don't even know if I will be able to compile with
> gromacs. Same thing for Gaussian. ORCA has no support for lam-mpi, and
> I don't know if I can hold two versions of mpi on my computers.
> I would really appreciate some suggestion know. I need to model an
> enzymatic reaction and was planning to do it using QM/MM. Actually, I
> am still planning, but I need just a bit of, let's say, guidance,
> right now.
> Thank you in advance
> 
> 
> >
> > Hi Stefan,
> >
> > unfortunately, cpmd-qmmm does not seem to be part of the standard
> > gromacs version. If you want to use it, you have to use some ancient
> > versions of gromacs and the patch from this page:
> > http://www.tougaloo.edu/research/qmmm/index.htm
> >
> > If you have a big QM box, the superiority of cpmd in scalability is
> > worth the afford of using an old GMX version. AFAIK there is no other
> > qmmm possibility if you want to use the planar wave technique (and
> > therefor the fantastic scalability). [Please correct me, if I am
> > wrong...]
> >
> > Greets,
> > Christian
> >
> > On Mon, 2010-05-31 at 20:49 -0300, Stefan Hoorman wrote:
> >> I've downloaded gromacs from the git repository. I type ./bootstrap
> >> and get loads of warnings like this
> >>
> >> configure.ac:414: warning: AC_CACHE_VAL(ac_m_cpu_7450, ...):
> >> suspicious cache-id, must contain _cv_ to be cached
> >> configure.ac:414: warning: AC_CACHE_VAL(ac_m_tune_970, ...):
> >> suspicious cache-id, must contain _cv_ to be cached
> >>
> >> Plus, when I type ./configure CFLAGS=-DGMX_QMMM_CPMD --with-qmmm-cpmd,
> >> configure runs fine except for this warning:
> >> configure: WARNING: unrecognized options: --with-qmmm-cpmd
> >>
> >> I figure that if ./configure does not recognize the cpmd option, there
> >> is no point in trying to compile gromacs with cpmd, I mean, the "make"
> >> command is not going to include cpmd, or is it?
> >> Some help on the matter would be appreciated.
> >> Thank you
> > --
> > M.Sc. Christian Seifert
> > Department of Biophysics
> > University of Bochum
> > ND 04/67
> > 44780 Bochum
> > Germany
> > Tel: +49 (0)234 32 28363
> > Fax: +49 (0)234 32 14626
> > E-Mail: cseifert at bph.rub.de
> > Web: http://www.bph.rub.de
> >
> >
-- 
M.Sc. Christian Seifert
Department of Biophysics
University of Bochum
ND 04/67
44780 Bochum
Germany
Tel: +49 (0)234 32 28363
Fax: +49 (0)234 32 14626
E-Mail: cseifert at bph.rub.de
Web: http://www.bph.rub.de