[gmx-users] QM/MM simulations (Mark Abraham) (Groenhof, Gerrit) (Clinton King)
ggroenh at gwdg.de
Thu Sep 1 12:08:31 CEST 2016
No, it also works in gmx5.
Don't use domain decomposition or the verlet scheme (use group based cut-off instead) and run a single thread (-nt 1)
Hope it works of you too,
Date: Wed, 31 Aug 2016 13:28:56 -0600
From: Clinton King <clintonking36 at chem.byu.edu>
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] QM/MM simulations (Mark Abraham) (Groenhof,
<CABUMFLLgMSpeEX72t1nveb3tTTRWhyjgbuk=k4KHZF7Q0M97VQ at mail.gmail.com>
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Is is true that the gau script available at http://wwwuser.gwdg.de/~
ggroenh/qmmm.html only works with gromacs versions < 5?
Brigham Young University
> 5. Re: QM/MM simulations (Mark Abraham) (Groenhof, Gerrit)
> Unless there are no atoms in the QM region, the QM energy should not be
> Can you confirm that mdrun writes an input file (input.com)? and gaussian
> is executed?
> If not, has gromacs been compiled with QMMM support
> Sadly, most of the QM/MM interfaces have been lacking a maintainer on the
> GROMACS side for quite a number of years. You should definitely be
> following http://wwwuser.gwdg.de/~ggroenh/qmmm.html closely.
> On Mon, Aug 29, 2016 at 9:36 PM Clinton King <clintonking36 at chem.byu.edu>
> > I'm performing a QM/MM (using Gaussian 09 and Gromacs 5.1.2) simulation
> > a single molecule of octanol in a box of water. In examining the standard
> > output, it appears that call to Gaussian is proceeding as expected, but
> > looking at the log file, it doesn't appear that quantum energy is being
> > communicated correctly, ie the output looks like the following:
> > Step Time Lambda
> > 7000 7.00000 0.00000
> > Energies (kJ/mol)
> > LJ (SR) Disper. corr. Coulomb (SR) Coul. recip.
> > Quantum En.
> > 2.45033e+04 -1.74106e+02 -1.86935e+05 6.68753e+01
> > Potential Kinetic En. Total Energy Temperature
> > Pres. DC (bar)
> > -1.62539e+05 3.00966e+04 -1.32443e+05 2.97582e+02
> > Pressure (bar) Constr. rmsd
> > -7.37300e+01 8.07450e-06
> > Notice that the entry for Quantum En. is 0.000.
> > Has anyone else seen this problem before? If so, what did you do about
> > --
> > Clinton King
> > Graduate Student
> > Chemistry Department
> > Brigham Young University
> > --
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