[gmx-users] interfacing with Gaussian 09 (Mark Abraham) (Groenhof, Gerrit)

[Clinton King]

Gerrit,

Thanks for your suggestions. I am using GROMACS 5.1.2.

After reading through your message, I realized that I was using GAUSS_DIR
and GAUSS_EXE for the location and name of the gau script instead of
GMX_QM_GAUSS_DIR and GMX_QM_GAUSS_EXE. So I changed that, and then I got
the error message from line 227 of qm_gaussian.c : "no
$GMX_QM_MODIFIED_LINKS_DIR, this is were the modified links reside."

I thought that one could use the gau script successfully without modifying
any Gaussian links.

I decided to try setting the GMX_QM_MODIFIED_LINKS_DIR environmental
variable to an empty folder. I am attaching the resulting output (as links
at the end of this message); both what was sent to stdout as well as the
gmx generated log file.

Looking through qm_gaussian.c, as well as the output I have so far, it
appears that modified Gaussian links *are* required for gmx to interface
with Gaussian.

So, the bottom line is that in order for Gromacs to interface with Gaussian
to perform a quantum molecular dynamics computation, I must have access to
the Gaussian source code. Is that correct?

https://drive.google.com/file/d/0B-W4G39j_Icjc21TcTN1S2M0MVk/view?usp=sharing
https://drive.google.com/file/d/0B-W4G39j_IcjZlVPb1NySkUtRDQ/view?usp=sharing

(Please let me know if the links above don't work.)

Thanks for your help

--
Clinton King
Graduate Student
Chemistry Department
Brigham Young University


> Message: 2
> Date: Sun, 12 Jun 2016 05:16:13 +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] interfacing with Gaussian 09 (Mark Abraham)
> Message-ID:
>         <858A7947BC0FE04DA05E1786A6D51D45263D61B2 at um-excdag-a05.um.gwdg.de
> >
> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
>
> Which version of Gmx are you using?
>
> I ask because of a recent bug fix. The bug was that I tried to print the
> value of an environment variable, without checking if that variable was
> set, causing set faulting.
>
> Make sure the GMX_QM_GAUSS_DIR (for Gmx < 5 GAUSS_DIR) are set and point
> to the location of the g09 directory.
>
> IN any case, for normal gaussian runs, the program should not write out
> the LJ.dat. IF the above does not help, you could perhaps send me the input
> (off list) and I can have a look at what goes wrong.
>
> Best,
>
> Gerrit
>
>
>
> Hi,
>
> Please don't subscribe to a digest if you're planning to reply to the
> digest and de-thread the discussion. Gerrit said the other week that gau
> works.
>
> Mark
>
> On Fri, 10 Jun 2016 18:18 Mark Abraham <mark.j.abraham at gmail.com> wrote:
>
> > Hi,
> >
> > Please check out http://wwwuser.gwdg.de/~ggroenh/qmmm.html and
> >
> http://www.gromacs.org/Downloads/Installation_Instructions/compiling_QMMM
> >
> > Mark
> >
> > On Fri, Jun 10, 2016 at 5:13 PM Clinton King <clintonking36 at chem.byu.edu
> >
> > wrote:
> >
> >> I'm having difficulty interfacing GROMACS with Gaussian 09. Is there
> >> anyone
> >> who has successfully done it who is willing to give some advice?
> >>
> >> --
> >> Clinton King
> >> Graduate Student
> >> Chemistry Department
> >> Brigham Young University
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
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> >>
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> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >>
> >
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 10 Jun 2016 14:27:01 -0600
> From: Clinton King <clintonking36 at chem.byu.edu>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: Re: [gmx-users] interfacing with Gaussian 09
> Message-ID:
>         <CABUMFLJBjWOgKGW0qUNFasGHUm_52f1k_RbHX=_
> sbUsJ_N9Q_g at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Sorry I forgot to change the subject line on my previous message; it was
> inadvertent. If Gerrit gets these emails maybe he can tell me what I'm
> doing wrong. Here are the symptoms:
>
> I'm using the gau script and I think the program is executing through until
> at least line 177 of the qm_gaussian.c code, as I see the message, "Level
> of SA at start = %d\n" in the output. However, soon after that, the process
> terminates with a segmentation fault. I think it is terminating before line
> 184 in the same code, as I don't believe the file LJ.dat is ever created.
>
> Maybe this means that the program isn't even getting to the point in which
> it calls up the gau script which in turn calls up Gaussian, since that
> happens on line 214 of the gm_gaussian.c code?
>
> Thanks in advance for any help anyone can offer..
>
> Clinton
>
>
>
>