[gmx-users] About the QM/MM MD of Gromacs

[Groenhof, Gerrit]

Dear Clinton,

Thanks for the information and your effort.

Keep in mind however, that the points at which you request the electrostatic forces are always in angstrom. Even if with units=bohr keyword. This awk command converts coordinates of the MM atoms, which gromacs passes on in Bohr, into the required Angstrom unit.

I therefore don't think that this is bug, but it will be highly appreciated if you can confirm this (or not ).

During testing the gau script produced same results (energy and gradients) as the QM/MM implementation with the modified gaussian.

best,

Gerrit


Date: Fri, 9 Sep 2016 10:03:49 -0600
From: Clinton King <clintonking36 at chem.byu.edu>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: Re: [gmx-users] About the QM/MM MD of Gromacs
Message-ID:
        <CABUMFLLsmduGm_i_6PUgwVbqapma1ApaotB6UigpGLYCz5qtoQ at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

An FYI: I have found some bugs in the awk scripting on (about) lines 59 and
71 of the gau script. The following two lines of awk code should fix those
bugs, but as soon as I am sure I have it working, I'll post the version of
the gau script that I am using to this forum in case anyone else wants to
use it.

awk -v nlines=0 '{if (nlines > 2 && $1) printf "%10.8f %10.8f %10.8f\n",
$2*0.529177249,$3*0.529177249,$4*0.529177249}{if ($1) ;else nlines++ }'
input.com >> temp.com

awk -v nlines=0 '{if (nlines > 2 && $1) print $1}{if ($1) ;else nlines++ }'
input.com >> MMcharges.txt

--
Clinton King
Graduate Student
Chemistry Department
Brigham Young University


>
> Today's Topics:
>
>    1. Re: About the QM/MM MD of Gromacs (???) (Timofey Tyugashev)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 9 Sep 2016 15:50:49 +0700
> From: Timofey Tyugashev <tyugashev at niboch.nsc.ru>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] About the QM/MM MD of Gromacs (???)
> Message-ID: <73e2df17-6226-35bd-688b-c1413bfce167 at niboch.nsc.ru>
> Content-Type: text/plain; charset=UTF-8; format=flowed
>
>
> So the only QM software that GROMACS can run for QMMM is Gaussian (09?),
> in single-thread CPU-only mode and with cut-off setting that's listed as
> depreciated, right?
> 08.09.2016 21:11, gromacs.org_gmx-users-request at maillist.sys.kth.se ?????:
> > Message: 3
> > Date: Thu, 8 Sep 2016 13:05:38 +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] About the QM/MM MD of Gromacs (???)
> > Message-ID:
> >       <858A7947BC0FE04DA05E1786A6D51D4533080324 at um-excdag-a05.um.gwdg.de
> >
> > Content-Type: text/plain; charset="us-ascii"
> >
> > Hi,
> >
> > Orca with gromacs >= 5 has not been tested and there are some
> indications that it is broken (redmine issue 1934).
> >
> > QM/MM with Gaussian is working, as long as you use a group based
> cut-offs and run mdrun on a single thread (-nt 1).
> >
> > I therefore recommend to use gaussian (with the gau script athttp://
> wwwuser.gwdg.de/~ggroenh/qmmm.html#gaussian  no source code of Gaussian
> is required), or stick to an older version of gromacs that supports ORCA.
> >
> > Best,
> >
> > Gerrit
> >
> >
> >
> >
> > Dear all:
> >      I want to do the QM/MM MD calculation by gromacs. ORCA is my QM
> program for QM/MM calculation. But how can I configure this option by cmake?
> >      For older version of gromacs, we just need to run the command:
> >      ./configure --with-qmmm-orca --without-qmmm-gaussian
> >      But for newer version of gromacs, we can only use the cmake to
> configure this option. Then how can I do? What is the command?
> >      Thank you!
> >      Best wishes,
> >      Junbo
>
>
>
>
>


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