[gmx-users] minimization is not converging
Justin Lemkul
jalemkul at vt.edu
Thu Sep 6 14:11:33 CEST 2018
On 9/6/18 8:04 AM, Bratin Kumar Das wrote:
> Respected Dr. Justin,
> Thanking you for your valuable advice.
> Actually, I also tried to minimised the protein alone in the solvent
> without the membrane. so, result was similar. The system bowed up
> similarly. Is it possible that due to inherent problem in topology this
> phenomena is happening.
Yes, but any sensible protein structure will not have such issues. Make
sure you haven't ignored warnings from pdb2gmx about missing residues,
long bonds, etc. that indicate problems with the structure. And again,
look at the mdrun output - it tells you where the largest forces are,
which is usually right where the problem is.
-Justin
> On Thu, Sep 6, 2018 at 5:20 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 9/6/18 7:47 AM, Bratin Kumar Das wrote:
>>
>>> Dear all,
>>> I am running a membrane simulation with GCGR protein. I am
>>> getting the following warning and error
>>>
>> Your system is unstable and blowing up. mdrun is telling you something is
>> really bad around atom 15058, so start looking there and follow advice at:
>> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#
>> Diagnosing_an_Unstable_System
>>
>> -Justin
>>
>>
>> gmx mdrun -v -s em_1.tpr -deffnm em_1
>>> :-) GROMACS - gmx mdrun, 2016.5 (-:
>>>
>>> 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/GR
>>> OMACS_projects/GROMACS_GCGR_new
>>> Command line:
>>> gmx mdrun -v -s em_1.tpr -deffnm em_1
>>>
>>>
>>> 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 em_1.tpr, VERSION 2016.5 (single precision)
>>> Using 1 MPI thread
>>> Using 4 OpenMP threads
>>>
>>>
>>> Steepest Descents:
>>> Tolerance (Fmax) = 1.00000e+01
>>> Number of steps = 2000
>>>
>>> WARNING: Listed nonbonded interaction between particles 19562 and 19566
>>> at distance 2.420 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.
>>>
>>>
>>>
>>> WARNING: Listed nonbonded interaction between particles 9914 and 9918
>>> at distance 2.232 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.
>>>
>>>
>>>
>>> WARNING: Listed nonbonded interaction between particles 29342 and 29348
>>> at distance 2.250 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= 1.42935e+20 Fmax= inf, atom=
>>> 15058
>>> Step= 1, Dmax= 1.0e-02 nm, Epot= 1.42929e+20 Fmax= inf, atom=
>>> 15058
>>> Step= 15, Dmax= 1.5e-06 nm, Epot= 1.42941e+20 Fmax= inf, atom=
>>> 15058
>>> Energy minimization has stopped, but the forces have not converged to the
>>> requested precision Fmax < 10 (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 16 steps,
>>> but did not reach the requested Fmax < 10.
>>> Potential Energy = 1.4292894e+20
>>> Maximum force = inf on atom 15058
>>> Norm of force = inf
>>>
>>> GROMACS reminds you: "Do not quench your inspiration and your imagination;
>>> do not become the slave of your model." (Vincent Van Gogh)
>>>
>> --
>> ==================================================
>>
>> 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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--
==================================================
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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