[gmx-users] energy minimization

[rose rahmani]

Hi,

I want to calculate the number of density profile of water.the initial .gro
file which i have,has amino acid in itself, which should not be present in
this analyze. So, i had to remove amino acid, and then, when i wanted to do
energy minimization again, it's crushed and gave me step files.
maybe it's because of modifying the initial gro file but i didn't have any
choice i think so! because i have another structures in initial.gro file
which i don't want to modify their coordinates.and all structure are in the
center of box and the rest of the box should be empty.
would you please help me? what is the alternative?

with regards




this is em.job

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+01
   Number of steps    =         5000
Step=    0, Dmax= 1.0e-02 nm, Epot= -6.05768e+04 Fmax= 1.07096e+04, atom=
815
Step=    1, Dmax= 1.0e-02 nm, Epot= -6.12124e+04 Fmax= 5.57695e+03, atom=
4307
Step=    2, Dmax= 1.2e-02 nm, Epot= -6.20952e+04 Fmax= 3.16416e+03, atom=
4307
Step=    3, Dmax= 1.4e-02 nm, Epot= -6.33594e+04 Fmax= 1.87516e+03, atom=
4302
Step=    4, Dmax= 1.7e-02 nm, Epot= -6.50390e+04 Fmax= 1.68178e+03, atom=
4303
Step=    5, Dmax= 2.1e-02 nm, Epot= -6.64168e+04 Fmax= 1.54347e+03, atom=
4303
Step=    6, Dmax= 2.5e-02 nm, Epot= -6.76032e+04 Fmax= 1.08368e+03, atom=
4303
Step=    7, Dmax= 3.0e-02 nm, Epot= -6.89478e+04 Fmax= 1.16283e+03, atom=
4303
Step=    8, Dmax= 3.6e-02 nm, Epot= -6.98965e+04 Fmax= 9.72829e+02, atom=
4303
Step=    9, Dmax= 4.3e-02 nm, Epot= -7.08234e+04 Fmax= 8.39105e+02, atom=
4303
Step=   10, Dmax= 5.2e-02 nm, Epot= -7.14550e+04 Fmax= 5.18546e+03, atom=
4302
Step=   11, Dmax= 6.2e-02 nm, Epot= -7.17534e+04 Fmax= 8.04910e+02, atom=
4302
Step=   12, Dmax= 7.4e-02 nm, Epot= -7.22134e+04 Fmax= 1.00656e+04, atom=
4301
Step=   13, Dmax= 8.9e-02 nm, Epot= -7.25685e+04 Fmax= 1.07787e+03, atom=
4303

step 14: Water molecule starting at atom 2018 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 14: Water molecule starting at atom 1265 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Step=   14, Dmax= 1.1e-01 nm, Epot=  2.77257e+05 Fmax= 2.29207e+09, atom=
2018^M
step 15: Water molecule starting at atom 1331 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Step=   15, Dmax= 5.3e-02 nm, Epot= -7.20611e+04 Fmax= 1.56839e+06, atom=
1331^MStep=   16, Dmax= 2.7e-02 nm, Epot= -7.28049e+04 Fmax= 4.98605e+02,
atom= 4301
Step=   17, Dmax= 3.2e-02 nm, Epot= -7.31402e+04 Fmax= 1.18628e+03, atom=
4303
Step=   18, Dmax= 3.9e-02 nm, Epot= -7.32653e+04 Fmax= 3.34851e+03, atom=
4301
Step=   19, Dmax= 4.6e-02 nm, Epot= -7.34325e+04 Fmax= 2.54904e+03, atom=
4301
Step=   20, Dmax= 5.5e-02 nm, Epot= -7.35292e+04 Fmax= 2.92387e+03, atom=
4301
Step=   21, Dmax= 6.7e-02 nm, Epot= -7.36418e+04 Fmax= 2.20184e+03, atom=
4301

                                       140,1
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