[gmx-users] Reg. minimization

[C.RAMYA]

Hello,

     I am trying to study a mutant lipase molecule. The complex[molecule +
spc water box] has shown +6 charge so i have neutralized the system
using genion. After that i am trying to minimize this.

The mdrun program gets done fine.. but i am having some doubts.
In the log file i do not get values for each step.. as you can see in step
3 and 5 given below [but this is case with many steps..n not in any
regular pattern] :

    "         Step           Time         Lambda
              3        3.00000        0.00000

           Step           Time         Lambda
              4        4.00000        0.00000

   Energies (kJ/mol)
           Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
    1.49416e+02    1.23777e+03    7.23143e+01    1.73961e+03    3.47387e+03
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
    1.86156e+04    8.90799e+04   -5.95683e+05   -9.39925e+04   -5.75307e+05
    Kinetic En.   Total Energy    Temperature Pressure (bar)
    0.00000e+00    0.00000e+00    0.00000e+00    0.00000e+00

           Step           Time         Lambda
              5        5.00000        0.00000

           Step           Time         Lambda
              6        6.00000        0.00000

   Energies (kJ/mol)
           Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
    2.06581e+02    1.18779e+03    7.22623e+01    1.73397e+03    3.45845e+03
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
    1.86006e+04    8.90886e+04   -5.95711e+05   -9.39880e+04   -5.75351e+05
    Kinetic En.   Total Energy    Temperature Pressure (bar)
    0.00000e+00    0.00000e+00    0.00000e+00    0.00000e+00

           Step           Time         Lambda
              7        7.00000        0.00000

   Energies (kJ/mol)
           Bond          Angle    Proper Dih. Ryckaert-Bell.          LJ-14
    1.95651e+02    1.18846e+03    7.23920e+01    1.73374e+03    3.43895e+03
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential
    1.85910e+04    8.91156e+04   -5.95729e+05   -9.39764e+04   -5.75369e+05
    Kinetic En.   Total Energy    Temperature Pressure (bar)
    0.00000e+00    0.00000e+00    0.00000e+00    0.00000e+00


    This is a run with 0.5 ps timestep and no. of steps as 1000 using
steep and PME interactions.[other options are default]

    I just wanted to confirm is there any specific reason for this..or is
it fine??

and the final output is -

  "Stepsize too small, or no change in energy.
   Converged to machine precision,
   but not to the requested precision Fmax < 10

   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)

   Steepest Descents converged to machine precision in 889 steps,
   but did not reach the requested Fmax < 10.
   Potential Energy  = -5.8063038e+05
   Maximum force     =  4.5843417e+02 on atom 418
   Norm of force     =  1.7805715e+03   "

   I have read about similar outputs in some papers... but i am actually
not clear if it is required to re-minimize with some changes or is it
fine??

Thanks,
   Ramya.