[gmx-users] gromacs.org_gmx-users Digest, Vol 139, Issue 45

Groenhof, Gerrit ggroenh at gwdg.de
Wed Nov 11 17:35:51 CET 2015

> Is the information in the link still valid? The page is dated 09.01.07,
> almost nine years ago, and refers to GROMACS 3.3. Much water has gone
> under the bridge since then.

Have you tried?

> On choice of division and methods: I'm trying to think hard about it and
> consult people experienced with QM. I have looked though several papers
> dealing with similar systems but with different software.
> I'm reasonably sure about what methods and bases I should use, but still
> very uncertain on how to configure and make it run properly.

Check out the tutorial on DNA: http://wwwuser.gwdg.de/%7Eggroenh/SaoCarlos2008/html/tutorial.html

> Message: 1
> Date: Tue, 10 Nov 2015 11:31:03 +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] 2. QM/MM (Timofey Tyugashev)
> Message-ID:
>       <858A7947BC0FE04DA05E1786A6D51D452633733B at um-excdag-a05.um.gwdg.de>
> Content-Type: text/plain; charset="us-ascii"
> I'm looking to try a QM/MM simulation for a protein-DNA system using
> Gussian09 & GROMACS 4.6 (these are available at the local cluster).
> Does anyone has any experience working and getting results in this
> environment? Are there any notable problems? Should I pay special
> attention to any particular topics?
> Hi,
> The easiest is to use the gau script athttp://wwwuser.gwdg.de/~ggroenh/qmmm.html#gaussian
> Concerning notable problems, the main issue is to decide your QM/MM division and QM method and verify the validity of your choices.
> best,
> Gerrit

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