[gmx-users] powercut command

Thu Apr 13 12:22:00 CEST 2017

On 4/13/17 6:19 AM, Anshul Lahariya wrote:
> now i got this error
>
>
> Program:     gmx mdrun, version 2016.2
> Source file: src/gromacs/mdlib/constr.cpp (line 167)
>
> Fatal error:
> Too many LINCS warnings (1000)
> If you know what you are doing you can adjust the lincs warning threshold in
> your mdp file
> or set the environment variable GMX_MAXCONSTRWARN to -1,
> but normally it is better to fix the problem
>
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> [root at dhcppc58 AhpE_MSH]#
>

You simulation is crashing and cannot be continued.  Consult 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

Also, do NOT do your normal work as root.  That is extremely dangerous.

-Justin

>
> On Thu, Apr 13, 2017 at 3:43 PM, Anshul Lahariya <anshullahariya17 at gmail.com
>> wrote:
>
>> thankss tasneem.
>>
>> let me try.
>>
>>
>> On Thu, Apr 13, 2017 at 3:40 PM, Anshul Lahariya <
>> anshullahariya17 at gmail.com> wrote:
>>
>>> powercut take place and md stops, so i want to continue my md
>>>
>>>
>>>
>>>
>>> [root at dhcppc58 AhpE_MSH]# gmx mdrun -v -s md_1_0.tpr -e md_1_0.edr -g
>>> md_1_0.log -o md_1_0.xtc -cpi md_1_0.cpt -cpo md_1_0.cpt -append
>>>                       :-) GROMACS - gmx mdrun, 2016.2 (-:
>>>
>>>                             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) 2001-2015, 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 2016.2
>>> Executable:   /usr/bin/gmx
>>> Data prefix:  /usr
>>> Working dir:  /home/anshu/Pharma/AhpE_MSH
>>> Command line:
>>>   gmx mdrun -v -s md_1_0.tpr -e md_1_0.edr -g md_1_0.log -o md_1_0.xtc
>>> -cpi md_1_0.cpt -cpo md_1_0.cpt -append
>>>
>>>
>>> -------------------------------------------------------
>>> Program:     gmx mdrun, version 2016.2
>>> Source file: src/gromacs/commandline/cmdlineparser.cpp (line 235)
>>> Function:    void gmx::CommandLineParser::parse(int*, char**)
>>>
>>> Error in user input:
>>> Invalid command-line options
>>>   In command-line option -o
>>>     File name 'md_1_0.xtc' cannot be used for this option.
>>>     Only the following extensions are possible:
>>>       .trr, .cpt, .tng
>>>
>>> For more information and tips for troubleshooting, please check the
>>> GROMACS
>>> website at http://www.gromacs.org/Documentation/Errors
>>> -------------------------------------------------------
>>> [root at dhcppc58 AhpE_MSH]# ^C
>>> [root at dhcppc58 AhpE_MSH]#
>>>
>>>
>>>
>>>
>>> plzzz help me and suggest me the command for continuation of my md run
>>>
>>> On Thu, Apr 13, 2017 at 3:34 PM, Tasneem Kausar <
>>> tasneemkausar12 at gmail.com> wrote:
>>>
>>>> please give the exact command and error message.
>>>>
>>>> On Thu, Apr 13, 2017 at 3:30 PM, Anshul Lahariya <
>>>> anshullahariya17 at gmail.com
>>>>> wrote:
>>>>
>>>>> dear das sir,
>>>>>
>>>>> -cpi was already added to the command but my problem is not solved
>>>>>
>>>>> On Thu, Apr 13, 2017 at 3:24 PM, Anshul Lahariya <
>>>>> anshullahariya17 at gmail.com
>>>>>> wrote:
>>>>>
>>>>>> error says, xtc file is not used for this option . plzz use trr,
>>>> cpt, tng
>>>>>>
>>>>>>
>>>>>> help me out
>>>>>>
>>>>>> On Thu, Apr 13, 2017 at 11:29 AM, Amir Zeb <zebamir85 at gmail.com>
>>>> wrote:
>>>>>>
>>>>>>> please put this command line
>>>>>>> gmx mdrun -v -s xxx.tpr -c xxx.gro -g xxx.log -e xxx.edr -cpi
>>>> xxx.cpt -o
>>>>>>> md_1_0.xtc
>>>>>>>
>>>>>>> good luck
>>>>>>>
>>>>>>> On Wed, Apr 12, 2017 at 10:42 PM, Anshul Lahariya <
>>>>>>> anshullahariya17 at gmail.com> wrote:
>>>>>>>
>>>>>>>> My md was running. Suddenly power supply was cuts due to some
>>>> reason
>>>>>>> and my
>>>>>>>> my MD stops..
>>>>>>>> To continue my MD, I use command:-
>>>>>>>>
>>>>>>>>
>>>>>>>> gmx mdrun -v -s 10ns.tpr -e 10ns.edr -g 10ns.log -10ns.xtc -cpi
>>>>> 10ns.cpt
>>>>>>>> -cpo 10ns.cpt -append
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> but shows error.
>>>>>>>>
>>>>>>>>
>>>>>>>> Error in user input:
>>>>>>>> Invalid command-line options
>>>>>>>>     Unknown command-line option -md_1_0.xtc
>>>>>>>>
>>>>>>>> For more information and tips for troubleshooting, please check
>>>> the
>>>>>>> GROMACS
>>>>>>>> website at http://www.gromacs.org/Documentation/Errors
>>>>>>>> -------------------------------------------------------
>>>>>>>> [root at dhcppc58 AhpE_MSH]#
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> Plzz.. help me out....
>>>>>>>> --
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>>>>>>
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>>

-- 
==================================================

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

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