[gmx-users] Re: Energy minimization output

[alkasrivastava at iitb.ac.in]

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.