Hi Cristoph, Thanks for the reply. I found that my problem was not gromacs. The input that ORCA was receiving from GROMACS did not have the correct number of hydrogens. I've solved this problem now and ORCA is running fine. I however ran into another problem with my energy minimization. The output from my gromacs log file is the following:
Step Time Lambda 0 0.00000 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 1.21899e+04 1.92496e+03 5.62567e+03 1.49141e+01 3.68001e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum En. 2.41200e+04 1.47494e+05 -5.06544e+05 -7.56009e+04 -3.96508e+06 Potential Pressure (bar) -4.35218e+06 -2.10629e+04 Step Time Lambda 1 1.00000 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 1.20006e+04 1.92297e+03 5.62600e+03 1.47801e+01 3.67746e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum En. 2.41174e+04 1.46421e+05 -5.06609e+05 -7.56156e+04 -4.00402e+06 Potential Pressure (bar) -4.39246e+06 -2.10739e+04 Step Time Lambda 2 2.00000 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 1.17961e+04 1.92126e+03 5.62633e+03 1.46477e+01 3.67461e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum En. 2.41145e+04 1.45528e+05 -5.06679e+05 -7.56315e+04 -4.18671e+06 Potential Pressure (bar) -4.57635e+06 -2.10854e+04 Step Time Lambda 3 3.00000 0.00000 Step Time Lambda 4 4.00000 0.00000 Energies (kJ/mol) Bond Angle Proper Dih. Improper Dih. LJ-14 1.16705e+04 1.92041e+03 5.62652e+03 1.45728e+01 3.67282e+03 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Quantum En. 2.41128e+04 1.45113e+05 -5.06721e+05 -7.56410e+04 -4.24486e+06 Potential Pressure (bar) -4.63509e+06 -2.10913e+04 Step Time Lambda 5 5.00000 0.00000 Step Time Lambda 6 6.00000 0.00000 Step Time Lambda 7 7.00000 0.00000 Step Time Lambda 8 8.00000 0.00000 Step Time Lambda 9 9.00000 0.00000 Step Time Lambda 10 10.00000 0.00000 Step Time Lambda 11 11.00000 0.00000 Step Time Lambda 12 12.00000 0.00000 Step Time Lambda 13 13.00000 0.00000 Step Time Lambda 14 14.00000 0.00000 Step Time Lambda 15 15.00000 0.00000 Step Time Lambda 16 16.00000 0.00000 Step Time Lambda 17 17.00000 0.00000 Step Time Lambda 18 18.00000 0.00000 Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested precision Fmax < 1000 Double precision normally gives you higher accuracy. You might need to increase your constraint accuracy, or turn off constraints alltogether (set constraints = none in mdp file) Why doesn't GROMACS output the energies for certain steps? Step 3 and steps 5-18 do show any output in the log file. Any ideas why this is happening? Thanks, Jose Tusell On Mon, Nov 14, 2011 at 7:05 AM, Christoph Riplinger <c...@thch.uni-bonn.de> wrote: > Dear Jose, > > I tried oniom which stopped for me either (although without a segfault). > Have you tried "QMMMscheme normal"? > > Christoph > > On 11/11/2011 05:53 PM, Jose Tusell wrote: >> >> Dear GROMACS users, >> >> I'm trying to run a QM-MM optimization. I solvate my protein and add >> ions then I do a classical optimization (just GROMACS). After that I >> run grompp with the following minim.mdp file (just showing qmmm >> options): >> >> QMMM = yes >> QMMM-grps = Other >> QMmethod = RHF >> QMbasis = 3-21G >> QMMMscheme = Oniom >> QMcharge = -1 >> QMmult = 1 >> SH = no >> >> This creates the *.tpr file that use to run mdrun. I use the >> following *.ORCAINFO file: >> >> !PAL8 Quick-DFT VerySlowConv >> %scf >> Maxiter 300 >> end >> %pal nprocs 8 >> end >> >> The ORCA run quickly converges but after that mdrun run stops with a >> segmentation fault. Am I missing something in all of this? Any help >> would be greatly appreciated. >> >> Thanks >> >> Jose Tusell > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists