I'm still working on the same problem I mentioned below. I'm trying to verify that I'm getting the right information out of Gromacs to send over to Gaussian (the input.com file). I might be misreading the "gau" script ( http://wwwuser.gwdg.de/~ggroenh/gau), but I think it's saying that there should be two coordinate sections: the first section should contain the cartesian coordinates for the QM atoms, while the second section should contain the coordinates for the MM atoms as a field of point charges.
I was attempting to simulate octanol in water solvent. The octanol atoms are to be treated by QM. I am pasting the body of the file in below. I can see that the MM coordinates were not included in the file. Has anyone seen this problem before? %chk=input %mem=1215752192 %subst l701 /fslhome/crk9/gromacs_src/modlinks/l701 %subst l301 /fslhome/crk9/gromacs_src/modlinks/l301 %subst l9999 /fslhome/crk9/gromacs_src/modlinks/l9999 #P DFT/3-21G* Nosymm units=bohr FORCE Punch=(Derivatives) iop(3/33=1) input-file generated by gromacs 0 1 1 62.2773850 18.0042321 12.8730289 8 62.7275929 19.6615469 13.5481707 1 60.8732094 22.8994305 14.4701237 1 61.3726754 22.4880551 11.2309538 6 60.8813102 21.4923398 12.9658582 1 58.3447012 18.6825131 11.6416004 1 56.8749667 21.5528031 12.3468668 6 58.2902482 20.2147180 13.0171607 1 55.7188751 17.8600687 15.1328293 1 58.8560031 18.0276177 16.2996878 6 57.3035799 19.1226107 15.5035981 1 58.1924753 22.3120539 17.8026816 1 55.1397300 22.2786189 16.7532522 6 56.5899874 21.0450109 17.5392182 1 54.3066933 18.3180812 19.3290486 1 57.3206195 18.3784025 20.4499142 6 55.7745716 19.6343339 19.9253595 1 56.0312610 22.6056363 22.6202497 1 52.9728344 22.2488265 21.3282668 6 54.6149342 21.2279325 22.0382414 1 55.1450509 17.9434118 24.4976697 1 51.9915096 19.0228103 24.2290069 6 53.9589936 19.6208130 24.3481110 1 55.7838078 22.2669272 26.6621999 1 54.5106599 19.8634027 28.4811908 1 52.4125626 22.0430645 27.4308446 6 54.1258397 21.0589621 26.8486065 -- Clinton King Graduate Student Chemistry Department Brigham Young University On Thu, Sep 1, 2016 at 7:03 AM, <gromacs.org_gmx-users-request @maillist.sys.kth.se> wrote: > > Today's Topics: > > 1. Re: QM/MM simulations (Mark Abraham) (Groenhof, Gerrit) > (Clinton King) (Groenhof, Gerrit) > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 1 Sep 2016 10:08:19 +0000 > 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] QM/MM simulations (Mark Abraham) (Groenhof, > Gerrit) (Clinton King) > Message-ID: > <858a7947bc0fe04da05e1786a6d51d453307f...@um-excdag-a05.um.gwdg.de > > > Content-Type: text/plain; charset="us-ascii" > > 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, > > Best, > > Gerrit > > > > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 31 Aug 2016 13:28:56 -0600 > From: Clinton King <clintonkin...@chem.byu.edu> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] QM/MM simulations (Mark Abraham) (Groenhof, > Gerrit) > Message-ID: > <CABUMFLLgMSpeEX72t1nveb3tTTRWhyjgbuk=k4khzf7q0m9...@mail.gm > ail.com> > Content-Type: text/plain; charset=UTF-8 > > Is is true that the gau script available at http://wwwuser.gwdg.de/~ > ggroenh/qmmm.html <http://wwwuser.gwdg.de/~ggroenh/qmmm.html> only works > with gromacs versions < 5? > > -- > Clinton King > Graduate Student > Chemistry Department > Brigham Young University > > > > > > > 5. Re: QM/MM simulations (Mark Abraham) (Groenhof, Gerrit) > > > > Hi, > > > > Unless there are no atoms in the QM region, the QM energy should not be > > zero. > > > > Can you confirm that mdrun writes an input file (input.com)? and > gaussian > > is executed? > > > > If not, has gromacs been compiled with QMMM support > > (GMX_QMMM_PROGRAM:STRING=gaussian)? > > > > Best, > > > > Gerrit > > > > > > Hi, > > > > 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. > > > > Mark > > > > On Mon, Aug 29, 2016 at 9:36 PM Clinton King <clintonkin...@chem.byu.edu > > > > wrote: > > > > > I'm performing a QM/MM (using Gaussian 09 and Gromacs 5.1.2) simulation > > of > > > 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 > > 0.00000e+00 > > > Potential Kinetic En. Total Energy > Temperature > > > Pres. DC (bar) > > > -1.62539e+05 3.00966e+04 -1.32443e+05 2.97582e+02 > > -2.34549e+01 > > > 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 > > it? > > > > > > -- > > > 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-requ...@gromacs.org.