That solved it. In the ORCA manual for version 2.8 it says to use bOpt = true instead of bOpt = yes. And there is no mention of the mdp option in the gromacs manual or gromacs online mdp options.
Ramon On Sun, Nov 20, 2011 at 4:57 PM, Jose Tusell <jrta1...@gmail.com> wrote: > I've tried the bOpt = true. Is the flag bOpt = yes? I'll try that > and I'll let you know. > > Ramon > > On Sun, Nov 20, 2011 at 1:19 PM, Christoph Riplinger > <c...@thch.uni-bonn.de> wrote: >> Dear Justin, >> >> The LJ and LJ.Excl files should be generated when you set bOpt = yes. What >> does the .inp file say. Is there !QMMMOpt or only !EnGrad? >> Christoph >> >> On 11/18/2011 06:20 PM, Jose Tusell wrote: >>> >>> Hi Justin, >>> >>> I tried using a larger step size but my system blew up... My guess is >>> that I have a bad starting structure, I'll work on the initial >>> structure for the QM region (energy minimize). >>> >>> When I'm running ORCA I want to have a LJ file to correct for the >>> interaction of my QM system with the protein. However this file is >>> not created when I run QMMM, I've used the bOpt = true in the mdp >>> file. Can anyone please offer some help on how to create this LJ >>> files? >>> >>> Thanks, >>> >>> Jose Tusell >>> >>> On Thu, Nov 17, 2011 at 2:07 PM, swati patel<swatipatel...@gmail.com> >>> wrote: >>>> >>>> hello, >>>> I am trying to simulate streptavidin tetramer-biotin complex.I ve >>>> calculated >>>> Ligand topology from a sofware PRODRG using gromos87 force fields.After >>>> solvating it,I am getting an error using grompp command >>>> >>>> Fatal error: >>>> Atomtype HW not found >>>> >>>> can anyone provide me some help? >>>> >>>> Thanx with anticipation. >>>> >>>> >>>> On Fri, Nov 18, 2011 at 2:29 AM, Jose Tusell<jrta1...@gmail.com> wrote: >>>>> >>>>> I'll try changing the step size first and if that fails I'll try >>>>> another algorithm. Thanks for the input. >>>>> >>>>> Jose Tusell >>>>> >>>>> On Thu, Nov 17, 2011 at 11:48 AM, Justin A. Lemkul<jalem...@vt.edu> >>>>> wrote: >>>>>> >>>>>> Jose Tusell wrote: >>>>>>> >>>>>>> Hi Justin, >>>>>>> >>>>>>> Thanks for the input on why this is happening. It sounds a little >>>>>>> suspicious that the energy doesn't change after a few steps of energy >>>>>>> minimization. Do you know of any way that I can find out what is >>>>>>> going on? >>>>>>> >>>>>> The screen output should indicate the atom with maximal force. >>>>>> Sometimes >>>>>> the EM algorithms get stuck when the geometry cannot change without >>>>>> making >>>>>> detrimental moves. You either need a larger step size, a different >>>>>> algorithm, or a better starting structure, if that is the case. I have >>>>>> seen >>>>>> this many times before, nothing suspicious about it. >>>>>> >>>>>> -Justin >>>>>> >>>>>>> Thanks, >>>>>>> >>>>>>> Jose Tusell >>>>>>> >>>>>>> On Thu, Nov 17, 2011 at 10:58 AM, Justin A. Lemkul<jalem...@vt.edu> >>>>>>> wrote: >>>>>>>> >>>>>>>> Jose Tusell wrote: >>>>>>>>> >>>>>>>>> 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? >>>>>>>>> >>>>>>>> This happens for the reasons printed by mdrun - those steps caused no >>>>>>>> change >>>>>>>> in energy. >>>>>>>> >>>>>>>> -Justin >>>>>>>> >>>>>>>> -- >>>>>>>> ======================================== >>>>>>>> >>>>>>>> Justin A. Lemkul >>>>>>>> Ph.D. Candidate >>>>>>>> ICTAS Doctoral Scholar >>>>>>>> MILES-IGERT Trainee >>>>>>>> Department of Biochemistry >>>>>>>> Virginia Tech >>>>>>>> Blacksburg, VA >>>>>>>> jalemkul[at]vt.edu | (540) 231-9080 >>>>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>>>>>>> >>>>>>>> ======================================== >>>>>>>> -- >>>>>>>> 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 >>>>>>>> >>>>>> -- >>>>>> ======================================== >>>>>> >>>>>> Justin A. Lemkul >>>>>> Ph.D. Candidate >>>>>> ICTAS Doctoral Scholar >>>>>> MILES-IGERT Trainee >>>>>> Department of Biochemistry >>>>>> Virginia Tech >>>>>> Blacksburg, VA >>>>>> jalemkul[at]vt.edu | (540) 231-9080 >>>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>>>>> >>>>>> ======================================== >>>>>> -- >>>>>> 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 >>>> >>>> -- >>>> 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 >> > -- 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
