[gmx-users] minimization_aborted
Bratin Kumar Das
177cy500.bratin at nitk.edu.in
Wed Aug 22 11:35:16 CEST 2018
Dear Alex
Can you please tell me how to pack a bilayer lipid
molecule around the protein. Because bad contact is coming due to the code
for shrinking the box. During minimization the lipid bilayer should move
from protein c-alpha atoms. If you have any paper related to that please
send me the link
On Wed 22 Aug, 2018, 11:26 AM Alex, <nedomacho at gmail.com> wrote:
> Before you go on to listen to bad advice and recompile Gromacs in double
> precision, the errors you're getting during minimization are _much_ more
> likely to come from a bad initial state of your system.
>
> Alex
>
>
> On 8/21/2018 11:51 PM, Bratin Kumar Das wrote:
> > 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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> >>> posting!
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> >>>
> >> --
> >> *Regards,*
> >> *Rahul *
> >> --
> >> Gromacs Users mailing list
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