[gmx-users] minimization_aborted
RAHUL SURESH
drrahulsuresh at gmail.com
Wed Aug 22 07:32:43 CEST 2018
Hi.
As gromacs suggested try double precision.
Thank you
On Wed, 22 Aug 2018 at 10:36 AM, Bratin Kumar Das <
177cy500.bratin at nitk.edu.in> wrote:
> 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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> under the terms of the GNU Lesser General Public License
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>
> GROMACS: gmx mdrun, version 2016.5
> Executable: /usr/local/gromacs/bin/gmx
> Data prefix: /usr/local/gromacs
> Working dir:
> /home/workstation/Documents/GROMACS_projects/g_protein_class_b_sim_gromacs
> 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=
> 3647
> Step= 1, Dmax= 1.0e-02 nm, Epot= 4.26666e+09 Fmax= 7.52956e+11, atom=
> 3647
> Step= 2, Dmax= 1.2e-02 nm, Epot= 1.33982e+08 Fmax= 1.49946e+10, atom=
> 2036
> Step= 3, Dmax= 1.4e-02 nm, Epot= 2.28974e+07 Fmax= 9.37337e+08, atom=
> 3647
> Step= 4, Dmax= 1.7e-02 nm, Epot= 4.48769e+06 Fmax= 3.34151e+07, atom=
> 13662
> Step= 5, Dmax= 2.1e-02 nm, Epot= 3.37628e+06 Fmax= 3.28448e+06, atom=
> 3645
> Step= 6, Dmax= 2.5e-02 nm, Epot= 3.10830e+06 Fmax= 1.71706e+06, atom=
> 6356
> Step= 7, Dmax= 3.0e-02 nm, Epot= 2.96689e+06 Fmax= 1.68266e+06, atom=
> 6356
> Step= 8, Dmax= 3.6e-02 nm, Epot= 2.83736e+06 Fmax= 1.63442e+06, atom=
> 6356
> Step= 9, Dmax= 4.3e-02 nm, Epot= 2.70582e+06 Fmax= 1.59406e+06, atom=
> 6356
> Step= 10, Dmax= 5.2e-02 nm, Epot= 2.57016e+06 Fmax= 6.10145e+06, atom=
> 68387
>
> 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=
> 6356
> Step= 13, Dmax= 3.7e-02 nm, Epot= 2.41877e+06 Fmax= 3.20637e+06, atom=
> 68387
> Step= 14, Dmax= 4.5e-02 nm, Epot= 2.39232e+06 Fmax= 1.51717e+06, atom=
> 6356
> Step= 15, Dmax= 5.3e-02 nm, Epot= 2.25380e+06 Fmax= 5.76014e+06, atom=
> 6358
> Step= 16, Dmax= 6.4e-02 nm, Epot= 2.23708e+06 Fmax= 1.48175e+06, atom=
> 6358
> Step= 17, Dmax= 7.7e-02 nm, Epot= 2.00861e+06 Fmax= 1.06806e+06, atom=
> 6358
> Step= 18, Dmax= 9.2e-02 nm, Epot= 1.89692e+06 Fmax= 3.69159e+06, atom=
> 6358
> Step= 19, Dmax= 1.1e-01 nm, Epot= 1.75521e+06 Fmax= 1.19996e+06, atom=
> 6358
> Step= 20, Dmax= 1.3e-01 nm, Epot= 1.47811e+06 Fmax= 3.67398e+06, atom=
> 8027
> Step= 22, Dmax= 8.0e-02 nm, Epot= 1.45234e+06 Fmax= 2.18802e+06, atom=
> 6356
> Step= 23, Dmax= 9.6e-02 nm, Epot= 1.42778e+06 Fmax= 1.22861e+07, atom=
> 6285
> Step= 24, Dmax= 1.2e-01 nm, Epot= 1.39384e+06 Fmax= 1.16780e+06, atom=
> 6358
> Step= 26, Dmax= 6.9e-02 nm, Epot= 1.22389e+06 Fmax= 1.01826e+06, atom=
> 6356
> Step= 27, Dmax= 8.3e-02 nm, Epot= 1.05663e+06 Fmax= 8.23676e+05, atom=
> 6358
> Step= 28, Dmax= 9.9e-02 nm, Epot= 9.00862e+05 Fmax= 4.41513e+06, atom=
> 6285
> Step= 30, Dmax= 6.0e-02 nm, Epot= 8.78491e+05 Fmax= 9.03216e+05, atom=
> 6356
> Step= 31, Dmax= 7.2e-02 nm, Epot= 7.32139e+05 Fmax= 8.20015e+05, atom=
> 6285
> Step= 32, Dmax= 8.6e-02 nm, Epot= 6.90801e+05 Fmax= 7.16405e+06, atom=
> 6285
> Step= 33, Dmax= 1.0e-01 nm, Epot= 6.01138e+05 Fmax= 7.02733e+05, atom=
> 6358
> Step= 34, Dmax= 1.2e-01 nm, Epot= 4.08422e+05 Fmax= 6.19177e+05, atom=
> 6356
> Step= 35, Dmax= 1.5e-01 nm, Epot= 2.39180e+05 Fmax= 8.93953e+06, atom=
> 6356
> Step= 36, Dmax= 1.8e-01 nm, Epot= 1.77754e+05 Fmax= 4.65642e+05, atom=
> 6356
> Step= 37, Dmax= 2.1e-01 nm, Epot= 9.49342e+03 Fmax= 7.65517e+06, atom=
> 6356
> Step= 39, Dmax= 1.3e-01 nm, Epot= -1.01297e+05 Fmax= 3.21496e+05, atom=
> 6357
>
> 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=
> 6532
> Step= 43, Dmax= 4.6e-02 nm, Epot= -1.94365e+05 Fmax= 2.98882e+05, atom=
> 6357
> Step= 44, Dmax= 5.5e-02 nm, Epot= -2.50520e+05 Fmax= 1.07420e+06, atom=
> 6551
> Step= 45, Dmax= 6.6e-02 nm, Epot= -2.65915e+05 Fmax= 2.73365e+05, atom=
> 6357
> Step= 46, Dmax= 8.0e-02 nm, Epot= -3.58321e+05 Fmax= 2.46276e+05, atom=
> 6357
> Step= 47, Dmax= 9.6e-02 nm, Epot= -4.33618e+05 Fmax= 6.66792e+05, atom=
> 6285
> Step= 48, Dmax= 1.1e-01 nm, Epot= -4.45739e+05 Fmax= 6.65627e+05, atom=
> 6285
>
> 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=
> 6285
> Step= 51, Dmax= 8.3e-02 nm, Epot= -5.04696e+05 Fmax= 2.93639e+06, atom=
> 6272
> Step= 52, Dmax= 9.9e-02 nm, Epot= -5.45904e+05 Fmax= 1.87021e+05, atom=
> 6357
> Step= 53, Dmax= 1.2e-01 nm, Epot= -6.52906e+05 Fmax= 2.72180e+05, atom=
> 6357
> Step= 55, Dmax= 7.1e-02 nm, Epot= -7.07692e+05 Fmax= 1.08267e+07, atom=
> 3569
> Step= 62, Dmax= 1.3e-03 nm, Epot= -7.60656e+05 Fmax= 1.19350e+08, atom=
> 11335
> Step= 65, Dmax= 4.0e-04 nm, Epot= -7.60669e+05 Fmax= 3.94493e+07, atom=
> 3569
> Step= 69, Dmax= 6.0e-05 nm, Epot= -7.60669e+05 Fmax= 1.55572e+07, atom=
> 35695
> Step= 70, Dmax= 7.2e-05 nm, Epot= -7.60670e+05 Fmax= 1.30303e+07, atom=
> 11335
> Step= 71, Dmax= 8.7e-05 nm, Epot= -7.60677e+05 Fmax= 2.11985e+07, atom=
> 3569
> Step= 72, Dmax= 1.0e-04 nm, Epot= -7.60678e+05 Fmax= 1.99492e+07, atom=
> 11335
> Step= 73, Dmax= 1.2e-04 nm, Epot= -7.60686e+05 Fmax= 2.93949e+07, atom=
> 3569
> Step= 74, Dmax= 1.5e-04 nm, Epot= -7.60686e+05 Fmax= 2.98387e+07, atom=
> 11335
> Step= 75, Dmax= 1.8e-04 nm, Epot= -7.60696e+05 Fmax= 4.12585e+07, atom=
> 3569
> Step= 83, Dmax= 1.7e-06 nm, Epot= -7.60696e+05 Fmax= 4.05617e+07, atom=
> 35695
> 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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--
*Regards,*
*Rahul *
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