[gmx-users] powercut command

Anshul Lahariya anshullahariya17 at gmail.com
Thu Apr 13 12:19:54 CEST 2017 

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]#


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....
>>> > >> > --
>>> > >> > Gromacs Users mailing list
>>> > >> >
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>>
>>
>

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