Thank you for reply.
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.
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.
Message: 1
Date: Tue, 10 Nov 2015 11:31:03 +
From: "Groenhof, Gerrit"<ggro...@gwdg.de>
To:"gromacs.org_gmx-users@maillist.sys.kth.se"
<gromacs.org_gmx-users@maillist.sys.kth.se>
Subject: Re: [gmx-users] 2. QM/MM (Timofey Tyugashev)
Message-ID:
<858a7947bc0fe04da05e1786a6d51d4526337...@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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