When I run gromacs with bOpt yes I run into the a problem with the coordinates of my qm system: the initial coordinates are the following:
NAME = ybu_em_qmmm.inp | 1> #input-file generated by gromacs | 2> !QMMMOpt TightSCF | 3> !PAL8 Quick-DFT VerySlowConv TightSCF KDIIS VDW EnGrad NoUseSym | 4> %scf | 5> Maxiter 5000 | 6> end | 7> %pal nprocs 8 | 8> end | 9> | 10> | 11> | 12> %LJCOEFFICIENTS "ybu_em_qmmm.LJ" | 13> *xyz -2 1 | 14> 7 46.4499998 40.2500010 48.1099987 | 15> 6 45.2400017 40.2899981 47.5600004 | 16> 7 44.7599983 40.6899977 46.3600016 | 17> 6 43.4700012 40.5999994 46.0599995 | 18> 7 42.6300001 40.1100016 46.9500017 | 19> 6 43.0100012 39.6799994 48.1699991 | 20> 7 42.1299982 39.1499996 49.0199995 | 21> 1 42.4300003 38.8100004 49.9200010 | 22> 1 41.1600018 39.0899992 48.7699986 | 23> 6 44.3400002 39.7700000 48.4999990 | 24> 7 45.0799990 39.4600010 49.5800018 | 25> 6 46.3500023 39.7600007 49.3499994 | 26> 6 47.7699995 40.5399990 47.4900007 | 27> 8 48.8000011 41.0900021 48.3400011 | 28> 6 49.8199987 41.7100000 47.4800014 | 29> 6 47.7400017 41.5500021 46.3600016 | 30> 8 46.9999981 41.4499998 45.1499987 | 31> 1 47.2300005 40.5999994 44.6799994 | 32> 6 49.1900015 41.9199991 46.1000013 | 33> 8 49.7800016 40.8699989 45.3399992 | 34> 1 50.7399988 41.0900021 45.1599979 | 35> 6 50.0799990 43.2399988 47.5799990 | 36> 8 51.4400005 43.5300016 47.9400015 | 37> 15 51.8400002 43.3099985 49.4799995 | 38> 8 52.1000004 44.8099995 49.9800014 | 39> 8 50.5700016 42.5000000 50.0600004 | 40> 8 53.1099987 42.3299980 49.3599987 | 41> 15 54.4700003 43.1799984 49.4500017 | 42> 8 55.5600023 42.1400023 48.8899994 | 43> 8 54.1200018 44.4799995 48.5599995 | 44> 8 54.5300007 43.5900021 50.9999990 | 45> 15 55.8799982 43.3500004 51.8499994 | 46> 8 57.0900011 43.9900017 50.9899998 | 47> 8 55.8300018 43.9099979 53.2200003 | 48> 8 56.1399984 41.7600012 51.8499994 | 49> 1 43.1099987 40.9200001 45.1000023 | 50> 1 47.1600008 39.6399999 50.0400019 | 51> 1 48.1400013 39.6199989 47.0900011 | 52> 1 47.3199987 42.4200010 46.8200016 | 53> 1 49.3300009 42.8999996 45.7000017 | 54> 1 50.7200003 41.1499977 47.4200010 | 55> 1 49.8600006 43.6999989 46.6300011 | 56> 1 49.4299984 43.6600018 48.3199978 | 57> 12 51.3999987 43.3799982 51.9299984 | 58> * | 59> %pointcharges "ybu_em_qmmm.pc" | 60> | 61> | 62> ****END OF INPUT**** This first calculation doesn't run into problems however after this the new coordinates are wrong by a factor of 10. This is the next input file generated by gromacs: NAME = ybu_em_qmmm.inp | 1> #input-file generated by gromacs | 2> !QMMMOpt TightSCF | 3> !PAL8 Quick-DFT VerySlowConv TightSCF KDIIS VDW EnGrad NoUseSym | 4> %scf | 5> Maxiter 5000 | 6> end | 7> %pal nprocs 8 | 8> end | 9> | 10> | 11> | 12> %LJCOEFFICIENTS "ybu_em_qmmm.LJ" | 13> *xyz -2 1 | 14> 7 4.6643215 4.0067959 4.8652828 | 15> 6 4.4694147 4.0687612 4.6910113 | 16> 7 4.4788954 4.0736303 4.5814043 | 17> 6 4.2882785 4.0960234 4.5192298 | 18> 7 4.1568694 3.9851558 4.6636197 | 19> 6 4.2702511 3.9942223 4.8413402 | 20> 7 4.1388491 3.8647231 4.9325246 | 21> 1 4.2422304 3.8729668 5.0225985 | 22> 1 4.0874949 3.9029175 4.8758829 | 23> 6 4.4479644 3.9264068 4.8907641 | 24> 7 4.4724247 3.8935867 5.0617158 | 25> 6 4.6581322 3.9623603 4.9860328 | 26> 6 4.7224784 3.9516553 4.7729388 | 27> 8 4.9013394 4.1037330 4.9433815 | 28> 6 5.0506485 4.1505158 4.7845429 | 29> 6 4.7479546 4.2596489 4.5867884 | 30> 8 4.6396983 4.1753584 4.3912268 | 31> 1 4.7245148 4.0333679 4.4395000 | 32> 6 4.9467531 4.1628179 4.5303190 | 33> 8 5.0127959 4.0332937 4.4357231 | 34> 1 5.0972128 4.1086709 4.5025694 | 35> 6 4.9707726 4.4155064 4.7358957 | 36> 8 5.1747119 4.3822494 4.7240046 | 37> 15 5.1759595 4.3526104 4.9696961 | 38> 8 5.2000558 4.5951414 5.0385225 | 39> 8 4.9872991 4.2056358 5.0856835 | 40> 8 5.3196424 4.1316289 4.9306369 | 41> 15 5.4781163 4.3365851 4.9144840 | 42> 8 5.6436682 4.1501650 4.8309124 | 43> 8 5.4556131 4.5460758 4.7758737 | 44> 8 5.4388809 4.3959689 5.1872373 | 45> 15 5.6339312 4.3419433 5.2184927 | 46> 8 5.8053279 4.4479111 5.0789297 | 47> 8 5.5981785 4.4297397 5.4245871 | 48> 8 5.6559128 4.0851763 5.2241915 | 49> 1 4.2944524 4.1013804 4.4863331 | 50> 1 4.7380015 3.9515409 5.0357658 | 51> 1 4.8261809 3.9258796 4.7002071 | 52> 1 4.7115117 4.2592505 4.6899751 | 53> 1 4.9388400 4.3221569 4.5484522 | 54> 1 5.1027077 4.0887082 4.7342393 | 55> 1 4.9870053 4.3987840 4.6446544 | 56> 1 4.9254298 4.3886098 4.8489299 | 57> 12 5.1316565 4.3423077 5.2266484 | 58> * | 59> %pointcharges "ybu_em_qmmm.pc" | 60> | 61> | 62> ****END OF INPUT**** Any ideas why this is happening? Thanks, Jose Tusell On Sun, Nov 20, 2011 at 5:03 PM, Jose Tusell <jrta1...@gmail.com> wrote: > 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
