[gmx-users] minimization_error

Sun Sep 9 20:53:11 CEST 2018

Dear all,
            During minimization of a protein molecule I found following
error
Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =        50000
Step=    0, Dmax= 1.0e-02 nm, Epot=  7.31298e+11 Fmax= 2.45648e+14, atom=
4054
Step=    1, Dmax= 1.0e-02 nm, Epot=  1.50885e+10 Fmax= 1.54878e+12, atom=
2379
Step=    2, Dmax= 1.2e-02 nm, Epot=  1.64698e+09 Fmax= 8.54330e+10, atom=
2383
Step=    3, Dmax= 1.4e-02 nm, Epot=  3.28739e+08 Fmax= 1.05704e+10, atom=
4048
Step=    4, Dmax= 1.7e-02 nm, Epot=  8.36090e+07 Fmax= 1.51995e+09, atom=
4050
Step=    5, Dmax= 2.1e-02 nm, Epot=  1.71898e+07 Fmax= 2.07116e+08, atom=
2389
Step=    6, Dmax= 2.5e-02 nm, Epot=  2.12858e+06 Fmax= 3.24305e+07, atom=
2429
Step=    7, Dmax= 3.0e-02 nm, Epot= -5.70125e+05 Fmax= 3.58609e+06, atom=
4049
Step=    8, Dmax= 3.6e-02 nm, Epot= -1.28016e+06 Fmax= 1.65686e+06, atom=
4049
Step=    9, Dmax= 4.3e-02 nm, Epot= -1.42968e+06 Fmax= 1.01298e+06, atom=
5961
Step=   10, Dmax= 5.2e-02 nm, Epot= -1.49528e+06 Fmax= 6.36454e+06, atom=
5961
Step=   11, Dmax= 6.2e-02 nm, Epot= -1.54938e+06 Fmax= 6.68748e+05, atom=
5961
Step=   12, Dmax= 7.4e-02 nm, Epot= -1.65446e+06 Fmax= 1.20563e+06, atom=
5961
Step=   13, Dmax= 8.9e-02 nm, Epot= -1.69075e+06 Fmax= 7.88571e+05, atom=
5961
Step=   14, Dmax= 1.1e-01 nm, Epot= -1.75037e+06 Fmax= 3.41886e+05, atom=
5959
Step=   15, Dmax= 1.3e-01 nm, Epot= -1.82276e+06 Fmax= 2.53773e+06, atom=
6040
Step=   16, Dmax= 1.5e-01 nm, Epot= -1.84616e+06 Fmax= 7.83228e+04, atom=
6038
Step=   17, Dmax= 1.8e-01 nm, Epot= -1.92394e+06 Fmax= 5.93584e+06, atom=
5959
Step=   18, Dmax= 2.2e-01 nm, Epot= -1.95719e+06 Fmax= 1.40285e+06, atom=
5959
Step=   22, Dmax= 3.3e-02 nm, Epot= -1.97156e+06 Fmax= 3.57269e+05, atom=
6035
Step=   23, Dmax= 4.0e-02 nm, Epot= -1.98878e+06 Fmax= 1.96496e+05, atom=
6038
Step=   24, Dmax= 4.8e-02 nm, Epot= -2.00989e+06 Fmax= 1.38405e+05, atom=
6038
Step=   25, Dmax= 5.8e-02 nm, Epot= -2.03060e+06 Fmax= 7.56408e+04, atom=
6038
Step=   26, Dmax= 6.9e-02 nm, Epot= -2.05304e+06 Fmax= 1.84679e+05, atom=
6035
Step=   27, Dmax= 8.3e-02 nm, Epot= -2.06081e+06 Fmax= 1.93408e+05, atom=
6035
Step=   28, Dmax= 9.9e-02 nm, Epot= -2.06913e+06 Fmax= 7.41533e+04, atom=
6035
Step=   29, Dmax= 1.2e-01 nm, Epot= -2.09293e+06 Fmax= 2.36608e+05, atom=
6035
Step=   30, Dmax= 1.4e-01 nm, Epot= -2.09915e+06 Fmax= 7.16045e+04, atom=
5956
Step=   32, Dmax= 8.6e-02 nm, Epot= -2.12024e+06 Fmax= 1.92532e+04, atom=
6034
Step=   33, Dmax= 1.0e-01 nm, Epot= -2.16233e+06 Fmax= 2.15331e+05, atom=
6034
Step=   34, Dmax= 1.2e-01 nm, Epot= -2.16784e+06 Fmax= 2.29221e+05, atom=
6034
Step=   35, Dmax= 1.5e-01 nm, Epot= -2.17775e+06 Fmax= 3.69837e+04, atom=
5954

step 36: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=   37, Dmax= 8.9e-02 nm, Epot= -2.19131e+06 Fmax= 6.98159e+04, atom=
5930
Step=   38, Dmax= 1.1e-01 nm, Epot= -2.20081e+06 Fmax= 6.51073e+04, atom=
5930
Step=   39, Dmax= 1.3e-01 nm, Epot= -2.20771e+06 Fmax= 5.28709e+04, atom=
5930
Step=   41, Dmax= 7.7e-02 nm, Epot= -2.21916e+06 Fmax= 4.40351e+04, atom=
6034
Step=   42, Dmax= 9.2e-02 nm, Epot= -2.22219e+06 Fmax= 8.88734e+04, atom=
6034
Step=   43, Dmax= 1.1e-01 nm, Epot= -2.23435e+06 Fmax= 4.54206e+04, atom=
6038
Step=   45, Dmax= 6.6e-02 nm, Epot= -2.24405e+06 Fmax= 2.58491e+04, atom=
6038
 Here you can see "step 36" why this warning is coming. To overcome that
what can be done ...please comment
after 2000 steps energy minimisation stopped..
Step= 1990, Dmax= 1.2e-02 nm, Epot= -2.65978e+06 Fmax= 1.04066e+04, atom=
7047
Step= 1991, Dmax= 1.5e-02 nm, Epot= -2.65979e+06 Fmax= 1.20911e+04, atom=
7047
Step= 1993, Dmax= 8.7e-03 nm, Epot= -2.65989e+06 Fmax= 1.40821e+03, atom=
7047
Step= 1994, Dmax= 1.0e-02 nm, Epot= -2.65990e+06 Fmax= 1.47325e+04, atom=
7047
Step= 1995, Dmax= 1.3e-02 nm, Epot= -2.66002e+06 Fmax= 4.74074e+03, atom=
7047
Step= 1997, Dmax= 7.5e-03 nm, Epot= -2.66004e+06 Fmax= 6.93813e+03, atom=
7047
Step= 1998, Dmax= 9.1e-03 nm, Epot= -2.66006e+06 Fmax= 7.07361e+03, atom=
7047
Step= 2000, Dmax= 5.4e-03 nm, Epot= -2.66010e+06 Fmax= 1.33089e+03, atom=
7047
Step= 2001, Dmax= 6.5e-03 nm, Epot= -2.66013e+06 Fmax= 8.79306e+03, atom=
7047
Step= 2002, Dmax= 7.8e-03 nm, Epot= -2.66019e+06 Fmax= 3.31993e+03, atom=
7047
Step= 2004, Dmax= 4.7e-03 nm, Epot= -2.66021e+06 Fmax= 3.95092e+03, atom=
7047
Step= 2005, Dmax= 5.6e-03 nm, Epot= -2.66022e+06 Fmax= 4.76073e+03, atom=
7047
Step= 2006, Dmax= 6.8e-03 nm, Epot= -2.66024e+06 Fmax= 5.70411e+03, atom=
7047
Step= 2007, Dmax= 8.1e-03 nm, Epot= -2.66025e+06 Fmax= 6.84219e+03, atom=
7047
Step= 2008, Dmax= 9.7e-03 nm, Epot= -2.66027e+06 Fmax= 8.21675e+03, atom=
7047
Step= 2009, Dmax= 1.2e-02 nm, Epot= -2.66027e+06 Fmax= 9.84435e+03, atom=
7047
Step= 2011, Dmax= 7.0e-03 nm, Epot= -2.66035e+06 Fmax= 9.95714e+02, atom=
7047

writing lowest energy coordinates.

Steepest Descents converged to Fmax < 1000 in 2012 steps
Potential Energy  = -2.6603498e+06
Maximum force     =  9.9571436e+02 on atom 7047
Norm of force     =  1.0860784e+01

GROMACS reminds you: "Only entropy comes easy." (Anton Chekov)
Is it a  indication of proper minimization ?

when I evaluated the energy of the system I found that the potential energy
of the system is
Steepest Descents converged to Fmax < 1000 in 2012 steps
Potential Energy  = -2.6603498e+06
Maximum force     =  9.9571436e+02 on atom 7047
Norm of force     =  1.0860784e+01