[gmx-users] minimization_aborted

Bratin Kumar Das 177cy500.bratin at nitk.edu.in
Wed Aug 22 07:06:38 CEST 2018

Dear All,
             I am simulating a membrane protein which have extracellular
domain, TMD(trans membrane domain) and a extracellular domain. After
packing the POPC molecules around the protein, I solvated  the system. I
removed all the waters from the POPC portion and added ions to neutralise
the system. During the energy minimisation the following errors are coming

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GROMACS:      gmx mdrun, version 2016.5
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:
Command line:
  gmx mdrun -v -s energy_minim.tpr -deffnm energy_minim

Running on 1 node with total 4 cores, 4 logical cores
Hardware detected:
  CPU info:
    Vendor: Intel
    Brand:  Intel(R) Xeon(R) CPU E3-1225 v5 @ 3.30GHz
    SIMD instructions most likely to fit this hardware: AVX2_256
    SIMD instructions selected at GROMACS compile time: AVX2_256

  Hardware topology: Basic

Reading file energy_minim.tpr, VERSION 2016.5 (single precision)
Using 1 MPI thread
Using 4 OpenMP threads

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+02
   Number of steps    =        50000

WARNING: Listed nonbonded interaction between particles 6334 and 6358
at distance 4.241 which is larger than the table limit 2.200 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.

Step=    0, Dmax= 1.0e-02 nm, Epot=  7.97855e+11 Fmax= 2.74610e+14, atom=
Step=    1, Dmax= 1.0e-02 nm, Epot=  4.26666e+09 Fmax= 7.52956e+11, atom=
Step=    2, Dmax= 1.2e-02 nm, Epot=  1.33982e+08 Fmax= 1.49946e+10, atom=
Step=    3, Dmax= 1.4e-02 nm, Epot=  2.28974e+07 Fmax= 9.37337e+08, atom=
Step=    4, Dmax= 1.7e-02 nm, Epot=  4.48769e+06 Fmax= 3.34151e+07, atom=
Step=    5, Dmax= 2.1e-02 nm, Epot=  3.37628e+06 Fmax= 3.28448e+06, atom=
Step=    6, Dmax= 2.5e-02 nm, Epot=  3.10830e+06 Fmax= 1.71706e+06, atom=
Step=    7, Dmax= 3.0e-02 nm, Epot=  2.96689e+06 Fmax= 1.68266e+06, atom=
Step=    8, Dmax= 3.6e-02 nm, Epot=  2.83736e+06 Fmax= 1.63442e+06, atom=
Step=    9, Dmax= 4.3e-02 nm, Epot=  2.70582e+06 Fmax= 1.59406e+06, atom=
Step=   10, Dmax= 5.2e-02 nm, Epot=  2.57016e+06 Fmax= 6.10145e+06, atom=

step 11: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

Back Off! I just backed up step11b.pdb to ./#step11b.pdb.3#

Back Off! I just backed up step11c.pdb to ./#step11c.pdb.3#
Wrote pdb files with previous and current coordinates
Step=   12, Dmax= 3.1e-02 nm, Epot=  2.52760e+06 Fmax= 1.57824e+06, atom=
Step=   13, Dmax= 3.7e-02 nm, Epot=  2.41877e+06 Fmax= 3.20637e+06, atom=
Step=   14, Dmax= 4.5e-02 nm, Epot=  2.39232e+06 Fmax= 1.51717e+06, atom=
Step=   15, Dmax= 5.3e-02 nm, Epot=  2.25380e+06 Fmax= 5.76014e+06, atom=
Step=   16, Dmax= 6.4e-02 nm, Epot=  2.23708e+06 Fmax= 1.48175e+06, atom=
Step=   17, Dmax= 7.7e-02 nm, Epot=  2.00861e+06 Fmax= 1.06806e+06, atom=
Step=   18, Dmax= 9.2e-02 nm, Epot=  1.89692e+06 Fmax= 3.69159e+06, atom=
Step=   19, Dmax= 1.1e-01 nm, Epot=  1.75521e+06 Fmax= 1.19996e+06, atom=
Step=   20, Dmax= 1.3e-01 nm, Epot=  1.47811e+06 Fmax= 3.67398e+06, atom=
Step=   22, Dmax= 8.0e-02 nm, Epot=  1.45234e+06 Fmax= 2.18802e+06, atom=
Step=   23, Dmax= 9.6e-02 nm, Epot=  1.42778e+06 Fmax= 1.22861e+07, atom=
Step=   24, Dmax= 1.2e-01 nm, Epot=  1.39384e+06 Fmax= 1.16780e+06, atom=
Step=   26, Dmax= 6.9e-02 nm, Epot=  1.22389e+06 Fmax= 1.01826e+06, atom=
Step=   27, Dmax= 8.3e-02 nm, Epot=  1.05663e+06 Fmax= 8.23676e+05, atom=
Step=   28, Dmax= 9.9e-02 nm, Epot=  9.00862e+05 Fmax= 4.41513e+06, atom=
Step=   30, Dmax= 6.0e-02 nm, Epot=  8.78491e+05 Fmax= 9.03216e+05, atom=
Step=   31, Dmax= 7.2e-02 nm, Epot=  7.32139e+05 Fmax= 8.20015e+05, atom=
Step=   32, Dmax= 8.6e-02 nm, Epot=  6.90801e+05 Fmax= 7.16405e+06, atom=
Step=   33, Dmax= 1.0e-01 nm, Epot=  6.01138e+05 Fmax= 7.02733e+05, atom=
Step=   34, Dmax= 1.2e-01 nm, Epot=  4.08422e+05 Fmax= 6.19177e+05, atom=
Step=   35, Dmax= 1.5e-01 nm, Epot=  2.39180e+05 Fmax= 8.93953e+06, atom=
Step=   36, Dmax= 1.8e-01 nm, Epot=  1.77754e+05 Fmax= 4.65642e+05, atom=
Step=   37, Dmax= 2.1e-01 nm, Epot=  9.49342e+03 Fmax= 7.65517e+06, atom=
Step=   39, Dmax= 1.3e-01 nm, Epot= -1.01297e+05 Fmax= 3.21496e+05, atom=

step 40: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

Back Off! I just backed up step40b.pdb to ./#step40b.pdb.2#

Back Off! I just backed up step40c.pdb to ./#step40c.pdb.2#
Wrote pdb files with previous and current coordinates
Step=   41, Dmax= 7.7e-02 nm, Epot= -1.70370e+05 Fmax= 1.79323e+06, atom=
Step=   43, Dmax= 4.6e-02 nm, Epot= -1.94365e+05 Fmax= 2.98882e+05, atom=
Step=   44, Dmax= 5.5e-02 nm, Epot= -2.50520e+05 Fmax= 1.07420e+06, atom=
Step=   45, Dmax= 6.6e-02 nm, Epot= -2.65915e+05 Fmax= 2.73365e+05, atom=
Step=   46, Dmax= 8.0e-02 nm, Epot= -3.58321e+05 Fmax= 2.46276e+05, atom=
Step=   47, Dmax= 9.6e-02 nm, Epot= -4.33618e+05 Fmax= 6.66792e+05, atom=
Step=   48, Dmax= 1.1e-01 nm, Epot= -4.45739e+05 Fmax= 6.65627e+05, atom=

step 49: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

Back Off! I just backed up step49b.pdb to ./#step49b.pdb.2#

Back Off! I just backed up step49c.pdb to ./#step49c.pdb.2#
Wrote pdb files with previous and current coordinates
Step=   50, Dmax= 6.9e-02 nm, Epot= -4.86014e+05 Fmax= 3.28474e+05, atom=
Step=   51, Dmax= 8.3e-02 nm, Epot= -5.04696e+05 Fmax= 2.93639e+06, atom=
Step=   52, Dmax= 9.9e-02 nm, Epot= -5.45904e+05 Fmax= 1.87021e+05, atom=
Step=   53, Dmax= 1.2e-01 nm, Epot= -6.52906e+05 Fmax= 2.72180e+05, atom=
Step=   55, Dmax= 7.1e-02 nm, Epot= -7.07692e+05 Fmax= 1.08267e+07, atom=
Step=   62, Dmax= 1.3e-03 nm, Epot= -7.60656e+05 Fmax= 1.19350e+08, atom=
Step=   65, Dmax= 4.0e-04 nm, Epot= -7.60669e+05 Fmax= 3.94493e+07, atom=
Step=   69, Dmax= 6.0e-05 nm, Epot= -7.60669e+05 Fmax= 1.55572e+07, atom=
Step=   70, Dmax= 7.2e-05 nm, Epot= -7.60670e+05 Fmax= 1.30303e+07, atom=
Step=   71, Dmax= 8.7e-05 nm, Epot= -7.60677e+05 Fmax= 2.11985e+07, atom=
Step=   72, Dmax= 1.0e-04 nm, Epot= -7.60678e+05 Fmax= 1.99492e+07, atom=
Step=   73, Dmax= 1.2e-04 nm, Epot= -7.60686e+05 Fmax= 2.93949e+07, atom=
Step=   74, Dmax= 1.5e-04 nm, Epot= -7.60686e+05 Fmax= 2.98387e+07, atom=
Step=   75, Dmax= 1.8e-04 nm, Epot= -7.60696e+05 Fmax= 4.12585e+07, atom=
Step=   83, Dmax= 1.7e-06 nm, Epot= -7.60696e+05 Fmax= 4.05617e+07, atom=
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 100 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.
You might need to increase your constraint accuracy, or turn
off constraints altogether (set constraints = none in mdp file)

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 84 steps,
but did not reach the requested Fmax < 100.
Potential Energy  = -7.6069581e+05
Maximum force     =  4.1258524e+07 on atom 3569
Norm of force     =  1.6956947e+05

GROMACS reminds you: "If you want to destroy my sweater, hold this thread
as I walk away." (Weezer)

I can't understand what is the problem inside the system. Because of this
reason I can't proceed to equilibration step. please help me.

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