[gmx-users] QM/MM simulations (Mark Abraham) (Groenhof, Gerrit) (Clinton King)

[Groenhof, Gerrit]

No, it also works in gmx5.

Don't use domain decomposition or the verlet scheme (use group based cut-off instead) and run a single thread (-nt 1)


Hope it works of you too,

Best,

Gerrit





----------------------------------------------------------------------

Message: 1
Date: Wed, 31 Aug 2016 13:28:56 -0600
From: Clinton King <clintonking36 at chem.byu.edu>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] QM/MM simulations (Mark Abraham) (Groenhof,
        Gerrit)
Message-ID:
        <CABUMFLLgMSpeEX72t1nveb3tTTRWhyjgbuk=k4KHZF7Q0M97VQ at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Is is true that the gau script available at http://wwwuser.gwdg.de/~
ggroenh/qmmm.html only works with gromacs versions < 5?

--
Clinton King
Graduate Student
Chemistry Department
Brigham Young University

>
>
>    5. Re: QM/MM simulations (Mark Abraham) (Groenhof, Gerrit)
>
> Hi,
>
> Unless there are no atoms in the QM region, the QM energy should not be
> zero.
>
> Can you confirm that mdrun writes an input file (input.com)? and gaussian
> is executed?
>
> If not, has gromacs been compiled with QMMM support
> (GMX_QMMM_PROGRAM:STRING=gaussian)?
>
> Best,
>
> Gerrit
>
>
> Hi,
>
> Sadly, most of the QM/MM interfaces have been lacking a maintainer on the
> GROMACS side for quite a number of years. You should definitely be
> following http://wwwuser.gwdg.de/~ggroenh/qmmm.html closely.
>
> Mark
>
> On Mon, Aug 29, 2016 at 9:36 PM Clinton King <clintonking36 at chem.byu.edu>
> wrote:
>
> > I'm performing a QM/MM (using Gaussian 09 and Gromacs 5.1.2) simulation
> of
> > a single molecule of octanol in a box of water. In examining the standard
> > output, it appears that call to Gaussian is proceeding as expected, but
> > looking at the log file, it doesn't appear that quantum energy is being
> > communicated correctly, ie the output looks like the following:
> >
> >
> >
> >            Step           Time         Lambda
> >            7000        7.00000        0.00000
> >
> >    Energies (kJ/mol)
> >         LJ (SR)          Disper. corr.       Coulomb (SR)   Coul. recip.
> >      Quantum En.
> >     2.45033e+04   -1.74106e+02   -1.86935e+05    6.68753e+01
> 0.00000e+00
> >       Potential          Kinetic En.         Total Energy    Temperature
> >      Pres. DC (bar)
> >    -1.62539e+05    3.00966e+04   -1.32443e+05    2.97582e+02
>  -2.34549e+01
> >  Pressure (bar)   Constr. rmsd
> >    -7.37300e+01    8.07450e-06
> >
> >
> > Notice that the entry for Quantum En. is 0.000.
> >
> > Has anyone else seen this problem before? If so, what did you do about
> it?
> >
> > --
> > Clinton King
> > Graduate Student
> > Chemistry Department
> > Brigham Young University
> > --