[gmx-users] Water molecule starting at atom 39087 can not be settled

liming_52 liming_52 at 163.com
Tue Mar 21 23:51:30 CET 2017

Dear Gromacs users,I am trying to run a md using 4n6p.cif obtained from PDB with a ligand. I converted the file into pdb format using DS4.1, and got the file named lactoferrin.pdb. When I directly run
the command "gmx mdrun -v -deffnm em", the program runs and produces the information as follows:
:-) GROMACS - gmx mdrun, VERSION 5.1.2 (-:

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

Running on 1 node with total 12 cores, 24 logical cores
Hardware detected:
  CPU info:
    Vendor: GenuineIntel
    Brand:  Intel(R) Xeon(R) CPU E5-2620 v2 @ 2.10GHz
    SIMD instructions most likely to fit this hardware: AVX_256
    SIMD instructions selected at GROMACS compile time: SSE2

Compiled SIMD instructions: SSE2, GROMACS could use AVX_256 on this machine, which is better

Reading file em.tpr, VERSION 5.1.2 (single precision)

Will use 18 particle-particle and 6 PME only ranks
This is a guess, check the performance at the end of the log file
Using 24 MPI threads
Using 1 OpenMP thread per tMPI thread

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =        50000
Step=    0, Dmax= 1.0e-03 nm, Epot=  2.62236e+13 Fmax= 1.19534e+16, atom= 3295
Step=    1, Dmax= 1.0e-03 nm, Epot=  1.08905e+13 Fmax= 4.61331e+15, atom= 3295
Step=    2, Dmax= 1.2e-03 nm, Epot=  4.10454e+12 Fmax= 1.60266e+15, atom= 3295
Step=    3, Dmax= 1.4e-03 nm, Epot=  1.40137e+12 Fmax= 5.00036e+14, atom= 3295
Step=    4, Dmax= 1.7e-03 nm, Epot=  4.33654e+11 Fmax= 1.40069e+14, atom= 3295
Step=    5, Dmax= 2.1e-03 nm, Epot=  1.22200e+11 Fmax= 3.52752e+13, atom= 3295
Step=    6, Dmax= 2.5e-03 nm, Epot=  3.18990e+10 Fmax= 8.01234e+12, atom= 3295
Step=    7, Dmax= 3.0e-03 nm, Epot=  8.21424e+09 Fmax= 1.64883e+12, atom= 3295
Step=    8, Dmax= 3.6e-03 nm, Epot=  2.50045e+09 Fmax= 3.09257e+11, atom= 3295
Step=    9, Dmax= 4.3e-03 nm, Epot=  9.40257e+08 Fmax= 6.82365e+10, atom= 3279
Step=   10, Dmax= 5.2e-03 nm, Epot=  2.72792e+08 Fmax= 1.39988e+10, atom= 3279
Step=   11, Dmax= 6.2e-03 nm, Epot=  5.92206e+07 Fmax= 2.62182e+09, atom= 3279
Step=   12, Dmax= 7.4e-03 nm, Epot=  1.69891e+07 Fmax= 4.55609e+08, atom= 3279
Step=   13, Dmax= 8.9e-03 nm, Epot=  4.88134e+06 Fmax= 1.13133e+08, atom= 3296
Step=   14, Dmax= 1.1e-02 nm, Epot=  1.86164e+06 Fmax= 3.65858e+07, atom= 3296
Step=   15, Dmax= 1.3e-02 nm, Epot=  6.44202e+05 Fmax= 1.40616e+07, atom= 3296
Step=   16, Dmax= 1.5e-02 nm, Epot=  2.16177e+05 Fmax= 4.49293e+06, atom= 3294
Step=   17, Dmax= 1.8e-02 nm, Epot=  2.88800e+04 Fmax= 2.99167e+06, atom= 134
Step=   18, Dmax= 2.2e-02 nm, Epot= -3.56134e+04 Fmax= 2.53958e+06, atom= 3296
Step=   19, Dmax= 2.7e-02 nm, Epot= -7.50786e+04 Fmax= 5.14618e+06, atom= 3296
Step=   20, Dmax= 3.2e-02 nm, Epot= -1.33736e+05 Fmax= 7.43406e+05, atom= 134
Step=   21, Dmax= 3.8e-02 nm, Epot= -1.68139e+05 Fmax= 6.44435e+06, atom= 3296
Step=   22, Dmax= 4.6e-02 nm, Epot= -2.39673e+05 Fmax= 3.99299e+05, atom= 3296
Step=   23, Dmax= 5.5e-02 nm, Epot= -3.07273e+05 Fmax= 1.60934e+06, atom= 3296
Step=   24, Dmax= 6.6e-02 nm, Epot= -3.25923e+05 Fmax= 2.64244e+05, atom= 3296
Step=   26, Dmax= 4.0e-02 nm, Epot= -3.66840e+05 Fmax= 1.58505e+05, atom= 1346
Step=   27, Dmax= 4.8e-02 nm, Epot= -3.98127e+05 Fmax= 6.82470e+05, atom= 134
Step=   28, Dmax= 5.7e-02 nm, Epot= -4.11327e+05 Fmax= 1.87577e+05, atom= 3297
Step=   29, Dmax= 6.9e-02 nm, Epot= -4.41304e+05 Fmax= 3.09908e+05, atom= 3297
Step=   30, Dmax= 8.2e-02 nm, Epot= -4.55118e+05 Fmax= 1.47622e+05, atom= 3297
Step=   31, Dmax= 9.9e-02 nm, Epot= -4.84124e+05 Fmax= 8.03024e+04, atom= 3296
Step=   32, Dmax= 1.2e-01 nm, Epot= -5.11472e+05 Fmax= 1.00688e+05, atom= 3296
Wrote pdb files with previous and current coordinates

Program gmx mdrun, VERSION 5.1.2
Source code file: /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/mdlib/constr.cpp, line: 555

Fatal error:

step 33: Water molecule starting at atom 39087 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

How can I solve this problem?


With my best wishes,
Ming Li, PhD
Chinese Academy of Agricultural Sciences, Beijing, China

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