[gmx-users] Re: Energy minimization output

[Kukol, Andreas]

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: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of alkasrivastava at iitb.ac.in
> Sent: 13 August 2008 10:26
> To: gmx-users at gromacs.org
> 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.
>
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