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

[Justin Lemkul]

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 (-:
>
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> Bjelkmar
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>    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
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> 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

==================================================