[gmx-users] powercut command
Anshul Lahariya
anshullahariya17 at gmail.com
Thu Apr 13 13:15:19 CEST 2017
okkk,,, thank u justin sir
On Thu, Apr 13, 2017 at 3:51 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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>>>>
>>>>
>>>
> --
> ==================================================
>
> 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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