[gmx-users] minimization_aborted
Alex
nedomacho at gmail.com
Wed Aug 22 22:05:18 CEST 2018
Protein-lipid assembly is one of the most common tasks in the field of
biomolecular simulation and tools exist. If your Google is as good as my
Google, this email provides help in terms of what to search for.
Alex
On 8/22/2018 3:34 AM, Bratin Kumar Das wrote:
> 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
>>>>>
>>>>> * Please search the archive at
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>>>>> posting!
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>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>
>>>> --
>>>> *Regards,*
>>>> *Rahul *
>>>> --
>>>> Gromacs Users mailing list
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