[gmx-users] QM/MM simulations

Wed Sep 7 23:47:00 CEST 2016

Nevermind, I figured out the answer to this question. Thanks!

--
Clinton King
Graduate Student
Chemistry Department
Brigham Young University

On Wed, Sep 7, 2016 at 1:14 PM, Clinton King <clintonking36 at chem.byu.edu>
wrote:

> 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.g
>> wdg.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
>> > > --
>>
>
>