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

[Andrian Saputra]

Make it easy with ORCA
Pada tanggal 14 Jun 2016 05.19, "Clinton King" <clintonking36 at chem.byu.edu>
menulis:

> 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!
> > >>
> > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >>
> > >> * For (un)subscribe requests visit
> > >> 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
> >
> >
> >
> >
> --
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