[gmx-users] minimization_aborted
Bratin Kumar Das
177cy500.bratin at nitk.edu.in
Wed Aug 22 07:51:35 CEST 2018
Dear Rahul,
Thinking you for your suggestion. I don't know how to
use double precision. can you please share some link for that
On Wed, Aug 22, 2018 at 11:02 AM, RAHUL SURESH <drrahulsuresh at gmail.com>
wrote:
> 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
> >
> >
> > GROMACS is written by:
> > Emile Apol Rossen Apostolov Herman J.C. Berendsen Par
> > Bjelkmar
> > Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit
> Groenhof
> > Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios
> > Karkoulis
> > Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
> > Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund
> > Teemu Murtola Szilard Pall Sander Pronk Roland Schulz
> > Alexey Shvetsov Michael Shirts Alfons Sijbers Peter
> Tieleman
> > Teemu Virolainen Christian Wennberg Maarten Wolf
> > and the project leaders:
> > Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
> >
> > Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> > Copyright (c) 2001-2017, The GROMACS development team at
> > Uppsala University, Stockholm University and
> > the Royal Institute of Technology, Sweden.
> > check out http://www.gromacs.org for more information.
> >
> > GROMACS is free software; you can redistribute it and/or modify it
> > under the terms of the GNU Lesser General Public License
> > as published by the Free Software Foundation; either version 2.1
> > of the License, or (at your option) any later version.
> >
> > 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.
> > --
> > Gromacs Users mailing list
> >
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> --
> *Regards,*
> *Rahul *
> --
> Gromacs Users mailing list
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