Your output looks like, that you are doing MD simulations, because a time in ps is reported. You should do energy minimisation first, use 'integrator = steep' in your .mdp file
Andreas > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > On Behalf Of [EMAIL PROTECTED] > Sent: 13 August 2008 10:26 > To: [email protected] > Subject: [gmx-users] Re: Energy minimization output > > Hi > > I am doing a 5 peptide simulation. > > I have done energy minimization using this command > > > 1.grompp -v -f em.mdp -c b4em_sol_mov1.gro -p gnnqqny.top -o em.tpr -nice 19 > > 2.mdrun -v -s em.tpr -e em.edr -c after_em.gro -o em.trr -g em.log -nice 19 > > > After energy minimization (steep, 5000 steps, emtol 100) i am getting some > pdb files referring to different steps of energy minimization as > outputalong with other standard output. when i checked the em.log file i > am getting > > > > > Step Time Lambda > 15 15.00000 0.00000 > > > t = 0.015 ps: Water molecule starting at atom 8264 can not be settled. > Check for bad contacts and/or reduce the timestep.Wrote pdb files with > previous and current coordinates > Step Time Lambda > 16 16.00000 0.00000 > > Energies (kJ/mol) > Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 > 9.98333e+04 1.36695e+04 1.52668e+03 1.78607e+03 4.70247e+03 > Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential > 2.55150e+03 3.77075e+05 -3.15610e+05 -2.36704e+04 1.61864e+05 > Kinetic En. Total Energy Temperature Pressure (bar) > 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 > > > t = 0.017 ps: Water molecule starting at atom 15071 can not be settled. > Check for bad contacts and/or reduce the timestep.Wrote pdb files with > previous and current coordinates > Step Time Lambda > 17 17.00000 0.00000 > > Step Time Lambda > 18 18.00000 0.00000 > > Energies (kJ/mol) > Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 > 9.45661e+04 1.37081e+04 1.40906e+03 1.82338e+03 3.67231e+03 > Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential > 2.53132e+03 3.24723e+05 -3.17639e+05 -2.36512e+04 1.01143e+05 > Kinetic En. Total Energy Temperature Pressure (bar) > 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 > > Step Time Lambda > 19 19.00000 0.00000 > > Energies (kJ/mol) > Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 > 8.03329e+04 1.30736e+04 1.41046e+03 1.92183e+03 3.32668e+03 > Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential > 2.50827e+03 2.64074e+05 -3.15758e+05 -2.36011e+04 2.72885e+04 > Kinetic En. Total Energy Temperature Pressure (bar) > 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 > > Step Time Lambda > 20 20.00000 0.00000 > > Energies (kJ/mol) > Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 > 6.75745e+04 1.25722e+04 1.34546e+03 1.92589e+03 3.23734e+03 > Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential > 2.47910e+03 2.34231e+05 -3.18011e+05 -2.35785e+04 -1.82240e+04 > Kinetic En. Total Energy Temperature Pressure (bar) > 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 > > > t = 0.021 ps: Water molecule starting at atom 15071 can not be settled. > Check for bad contacts and/or reduce the timestep.Wrote pdb files with > previous and current coordinates > Step Time Lambda > 21 21.00000 0.00000 > > Step Time Lambda > 22 22.00000 0.00000 > > Energies (kJ/mol) > Bond Angle Proper Dih. Ryckaert-Bell. LJ-14 > 5.69021e+04 1.19959e+04 1.30660e+03 1.92492e+03 3.11441e+03 > Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential > 2.47034e+03 2.13147e+05 -3.18361e+05 -2.35596e+04 -5.10587e+04 > Kinetic En. Total Energy Temperature Pressure (bar) > 0.00000e+00 0.00000e+00 0.00000e+00 0.00000e+00 > > > This is upto 40 ns after that i am not getting anything like that. I don't > know exactly what it mean and how could i get rid of such messages.I don't > know how to deal with it. > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
