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
