Nevermind, I figured out the answer to this question. Thanks! -- Clinton King Graduate Student Chemistry Department Brigham Young University
On Wed, Sep 7, 2016 at 1:14 PM, Clinton King <clintonkin...@chem.byu.edu> wrote: > 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.g >> wdg.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.