[gmx-users] Query regarding energy minimization step (step 12: Water molecule starting at atom 13529 can not be settled.)

Sat Mar 12 14:53:12 CET 2016

Thank you!

SHRI KANT
M Tech (Computational Biology)
Centre for Biotechnology
Anna University, Chennai
600025

On Fri, Mar 11, 2016 at 6:24 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/11/16 2:50 AM, shrikant kaushik wrote:
>
>> Dear all gromacs users,
>>                                    [shrikant at Ares Simulation]$ gmx-5.1.2
>> mdrun -v -deffnm em
>>                     :-) GROMACS - gmx mdrun, VERSION 5.1.2 (-:
>>
>>                              GROMACS is written by:
>>       Emile Apol      Rossen Apostolov  Herman J.C. Berendsen    Par
>> Bjelkmar
>>   Aldert van Buuren   Rudi van Drunen     Anton Feenstra   Sebastian
>> Fritsch
>>    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) 2001-2015, 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 5.1.2
>> Executable:   /usr/local/gromacs-5.1.2/bin/gmx-5.1.2
>> Data prefix:  /usr/local/gromacs-5.1.2
>> Command line:
>>    gmx-5.1.2 mdrun -v -deffnm em
>>
>>
>> Running on 1 node with total 4 cores, 4 logical cores
>> Hardware detected:
>>    CPU info:
>>      Vendor: GenuineIntel
>>      Brand:  Intel(R) Core(TM) i5-2400 CPU @ 3.10GHz
>>      SIMD instructions most likely to fit this hardware: AVX_256
>>      SIMD instructions selected at GROMACS compile time: AVX_256
>>
>> Reading file em.tpr, VERSION 5.1.2 (single precision)
>> Using 1 MPI thread
>> Using 4 OpenMP threads
>>
>>
>> Steepest Descents:
>>     Tolerance (Fmax)   =  1.00000e+03
>>     Number of steps    =        50000
>> Step=    0, Dmax= 1.0e-02 nm, Epot=  1.64486e+07 Fmax= 3.27208e+07, atom=
>> 4176
>> Step=    1, Dmax= 1.0e-02 nm, Epot=  1.55865e+07 Fmax= 3.13386e+07, atom=
>> 4176
>> Step=    2, Dmax= 1.2e-02 nm, Epot=  1.46513e+07 Fmax= 2.97319e+07, atom=
>> 4176
>> Step=    3, Dmax= 1.4e-02 nm, Epot=  1.36016e+07 Fmax= 2.78772e+07, atom=
>> 4176
>> Step=    4, Dmax= 1.7e-02 nm, Epot=  1.24230e+07 Fmax= 2.57543e+07, atom=
>> 4176
>> Step=    5, Dmax= 2.1e-02 nm, Epot=  1.11113e+07 Fmax= 2.33503e+07, atom=
>> 4176
>> Step=    6, Dmax= 2.5e-02 nm, Epot=  9.67180e+06 Fmax= 2.06643e+07, atom=
>> 4176
>> Step=    7, Dmax= 3.0e-02 nm, Epot=  8.12309e+06 Fmax= 1.77136e+07, atom=
>> 4176
>> Step=    8, Dmax= 3.6e-02 nm, Epot=  6.50058e+06 Fmax= 1.45408e+07, atom=
>> 4176
>> Step=    9, Dmax= 4.3e-02 nm, Epot=  4.86276e+06 Fmax= 1.12217e+07, atom=
>> 4176
>> Step=   10, Dmax= 5.2e-02 nm, Epot=  3.30460e+06 Fmax= 7.87434e+06, atom=
>> 4176
>> Step=   11, Dmax= 6.2e-02 nm, Epot=  2.04717e+06 Fmax= 9.25255e+06, atom=
>> 75560
>> Wrote pdb files with previous and current coordinates
>>
>> -------------------------------------------------------
>> Program gmx mdrun, VERSION 5.1.2
>> Source code file:
>> /usr/local/src/gromacs-5.1.2/src/gromacs/mdlib/constr.cpp, line: 555
>>
>> Fatal error:
>>
>> step 12: Water molecule starting at atom 13529 can not be settled.
>> Check for bad contacts and/or reduce the timestep if appropriate.
>>
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>>
>
>
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
>
> Since it's EM that's failing, the most likely problem is unreasonable
> coordinates (mdrun is printing out likely locations of these nasty
> interactions!).  Since you've provided no other useful information about
> what you're doing or what your system is, that's the best advice that can
> be given.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> 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.
>