[gmx-users] Query regarding energy minimization step (step 12: Water molecule starting at atom 13529 can not be settled.)

shrikant kaushik shrikant92pharmacy at gmail.com
Fri Mar 11 08:50:28 CET 2016

Dear all gromacs users,
                                  [shrikant at Ares Simulation]$ gmx-5.1.2
mdrun -v -deffnm em
                   :-) GROMACS - gmx mdrun, VERSION 5.1.2 (-:

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GROMACS:      gmx mdrun, VERSION 5.1.2
Executable:   /usr/local/gromacs-5.1.2/bin/gmx-5.1.2
Data prefix:  /usr/local/gromacs-5.1.2
Command line:
  gmx-5.1.2 mdrun -v -deffnm em

Running on 1 node with total 4 cores, 4 logical cores
Hardware detected:
  CPU info:
    Vendor: GenuineIntel
    Brand:  Intel(R) Core(TM) i5-2400 CPU @ 3.10GHz
    SIMD instructions most likely to fit this hardware: AVX_256
    SIMD instructions selected at GROMACS compile time: AVX_256

Reading file em.tpr, VERSION 5.1.2 (single precision)
Using 1 MPI thread
Using 4 OpenMP threads

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =        50000
Step=    0, Dmax= 1.0e-02 nm, Epot=  1.64486e+07 Fmax= 3.27208e+07, atom=
Step=    1, Dmax= 1.0e-02 nm, Epot=  1.55865e+07 Fmax= 3.13386e+07, atom=
Step=    2, Dmax= 1.2e-02 nm, Epot=  1.46513e+07 Fmax= 2.97319e+07, atom=
Step=    3, Dmax= 1.4e-02 nm, Epot=  1.36016e+07 Fmax= 2.78772e+07, atom=
Step=    4, Dmax= 1.7e-02 nm, Epot=  1.24230e+07 Fmax= 2.57543e+07, atom=
Step=    5, Dmax= 2.1e-02 nm, Epot=  1.11113e+07 Fmax= 2.33503e+07, atom=
Step=    6, Dmax= 2.5e-02 nm, Epot=  9.67180e+06 Fmax= 2.06643e+07, atom=
Step=    7, Dmax= 3.0e-02 nm, Epot=  8.12309e+06 Fmax= 1.77136e+07, atom=
Step=    8, Dmax= 3.6e-02 nm, Epot=  6.50058e+06 Fmax= 1.45408e+07, atom=
Step=    9, Dmax= 4.3e-02 nm, Epot=  4.86276e+06 Fmax= 1.12217e+07, atom=
Step=   10, Dmax= 5.2e-02 nm, Epot=  3.30460e+06 Fmax= 7.87434e+06, atom=
Step=   11, Dmax= 6.2e-02 nm, Epot=  2.04717e+06 Fmax= 9.25255e+06, atom=
Wrote pdb files with previous and current coordinates

Program gmx mdrun, VERSION 5.1.2
Source code file:
/usr/local/src/gromacs-5.1.2/src/gromacs/mdlib/constr.cpp, line: 555

Fatal error:

step 12: Water molecule starting at atom 13529 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
M Tech (Computational Biology)
Centre for Biotechnology
Anna University, Chennai

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