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?
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 > -- 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
