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! 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