[gmx-users] QM/MM simulations
Clinton King
clintonking36 at chem.byu.edu
Wed Sep 7 21:14:27 CEST 2016
I'm still working on the same problem I mentioned below. I'm trying to
verify that I'm getting the right information out of Gromacs to send over
to Gaussian (the input.com file). I might be misreading the "gau" script (
http://wwwuser.gwdg.de/~ggroenh/gau), but I think it's saying that there
should be two coordinate sections: the first section should contain the
cartesian coordinates for the QM atoms, while the second section should
contain the coordinates for the MM atoms as a field of point charges.
I was attempting to simulate octanol in water solvent. The octanol atoms
are to be treated by QM. I am pasting the body of the file in below. I can
see that the MM coordinates were not included in the file. Has anyone seen
this problem before?
%chk=input
%mem=1215752192
%subst l701 /fslhome/crk9/gromacs_src/modlinks/l701
%subst l301 /fslhome/crk9/gromacs_src/modlinks/l301
%subst l9999 /fslhome/crk9/gromacs_src/modlinks/l9999
#P DFT/3-21G*
Nosymm units=bohr
FORCE Punch=(Derivatives) iop(3/33=1)
input-file generated by gromacs
0 1
1 62.2773850 18.0042321 12.8730289
8 62.7275929 19.6615469 13.5481707
1 60.8732094 22.8994305 14.4701237
1 61.3726754 22.4880551 11.2309538
6 60.8813102 21.4923398 12.9658582
1 58.3447012 18.6825131 11.6416004
1 56.8749667 21.5528031 12.3468668
6 58.2902482 20.2147180 13.0171607
1 55.7188751 17.8600687 15.1328293
1 58.8560031 18.0276177 16.2996878
6 57.3035799 19.1226107 15.5035981
1 58.1924753 22.3120539 17.8026816
1 55.1397300 22.2786189 16.7532522
6 56.5899874 21.0450109 17.5392182
1 54.3066933 18.3180812 19.3290486
1 57.3206195 18.3784025 20.4499142
6 55.7745716 19.6343339 19.9253595
1 56.0312610 22.6056363 22.6202497
1 52.9728344 22.2488265 21.3282668
6 54.6149342 21.2279325 22.0382414
1 55.1450509 17.9434118 24.4976697
1 51.9915096 19.0228103 24.2290069
6 53.9589936 19.6208130 24.3481110
1 55.7838078 22.2669272 26.6621999
1 54.5106599 19.8634027 28.4811908
1 52.4125626 22.0430645 27.4308446
6 54.1258397 21.0589621 26.8486065
--
Clinton King
Graduate Student
Chemistry Department
Brigham Young University
On Thu, Sep 1, 2016 at 7:03 AM, <gromacs.org_gmx-users-request
@maillist.sys.kth.se> wrote:
>
> Today's Topics:
>
> 1. Re: QM/MM simulations (Mark Abraham) (Groenhof, Gerrit)
> (Clinton King) (Groenhof, Gerrit)
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 1 Sep 2016 10:08:19 +0000
> From: "Groenhof, Gerrit" <ggroenh at gwdg.de>
> To: "gromacs.org_gmx-users at maillist.sys.kth.se"
> <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] QM/MM simulations (Mark Abraham) (Groenhof,
> Gerrit) (Clinton King)
> Message-ID:
> <858A7947BC0FE04DA05E1786A6D51D453307FF99 at um-excdag-a05.um.gwdg.de
> >
> Content-Type: text/plain; charset="us-ascii"
>
> 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.gm
> ail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Is is true that the gau script available at http://wwwuser.gwdg.de/~
> ggroenh/qmmm.html <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
> > > --
>
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