[gmx-users] minimization_aborted
RAHUL SURESH
drrahulsuresh at gmail.com
Wed Aug 22 15:46:56 CEST 2018
Thank you Dr. Justin. Will keep a note on it.
On Wed, 22 Aug 2018 at 5:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 8/22/18 2:26 AM, RAHUL SURESH wrote:
> > Dear Bratin,
> >
> > See documentation for installation of gromacs with double precision. You
> > can always have gromacs installed with various versions. There is no need
> > to recompile, just have another source with double precision. Try it if
> it
> > doesn’t work better you will other good advices too. Hope gromacs don’t
> > suggest if it’s unlikely useful.
> >
> > Thank you
> >
> > More, I think here everyone suggest based on their own experiences.
>
> Yes, but great care is needed to not tell someone to do something
> unproductive. The magnitude of forces the OP reports are not going to be
> resolved by double precision code. GROMACS programs can't think for the
> user, so error messages often include generic advice that *might* be
> relevant. For mdrun, if convergence criteria aren't met, that suggestion
> is printed. But forces of 10^7 clearly indicate something pathological
> with the system.
>
> -Justin
>
> >
> >
> > On Wed, 22 Aug 2018 at 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
> >>>>>
> >>>>> * Please search the archive at
> >>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >>>>> posting!
> >>>>>
> >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>>>
> >>>>> * For (un)subscribe requests visit
> >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> >>>>> send a mail to gmx-users-request at gromacs.org.
> >>>>>
> >>>> --
> >>>> *Regards,*
> >>>> *Rahul *
> >>>> --
> >>>> Gromacs Users mailing list
> >>>>
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> >>>> Support/Mailing_Lists/GMX-Users_List before posting!
> >>>>
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> >>>> send a mail to gmx-users-request at gromacs.org.
> >>>>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
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> >> posting!
> >>
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> >> send a mail to gmx-users-request at gromacs.org.
> >>
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
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--
*Regards,*
*Rahul *
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