[gmx-users] Query regarding energy minimization step (step 12: Water molecule starting at atom 13529 can not be settled.)
shrikant kaushik
shrikant92pharmacy at gmail.com
Tue Mar 15 09:39:01 CET 2016
Dear all gromacs users,
I am trying to run simulation for my Phophorylated threonin
(TPO at 172 position in A chain og 4CFF
pdb id), I have generate topology using Prodrg2server. Then i try to run
energy minimization step its showing following error--
1. step 12: Water molecule starting at atom 13529 can not be settled.
2. Check for bad contacts and/or reduce the timestep if appropriate.
Currently i`m using GROMACS-5.1.2 and GROMOS 54a7 Force Field.
4cff_tpo topology problen
<https://docs.google.com/folderview?id=0B5ZuMCbMS3QNRDlQRm5HUllJSm8&usp=drive_web>
I have attached the files i used in simulation.
SHRI KANT
M Tech (Computational Biology)
Centre for Biotechnology
Anna University, Chennai
600025
On Sat, Mar 12, 2016 at 7:23 PM, shrikant kaushik <
shrikant92pharmacy at gmail.com> wrote:
> 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
>>
>> ==================================================
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