[gmx-users] powercut command
Anshul Lahariya
anshullahariya17 at gmail.com
Thu Apr 13 21:14:17 CEST 2017
i am performing a md of protein ligand complex for 10 ns.
i am using gromacs 5.1.4 on my lappy with 16 gb ram without gpu.
i was performing all the steps without error but found an error in mdrun.
kindly help me to stable my system.
{i am following the protein - ligand complex tutorial of bevan lab}
On Thu, Apr 13, 2017 at 9:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 4/13/17 11:25 AM, Anshul Lahariya wrote:
>
>> i was failed to diagnose. plzz help me
>>
>>
> Start here:
>
> http://www.catb.org/esr/faqs/smart-questions.html
>
> As I already said, no one on this list can tell anything about your system
> because you have provided no useful diagnostic information or description
> of what you're doing. If you want free help, you have to make it easy for
> people to help you, with clear, concise communication about what you are
> doing.
>
> -Justin
>
> On Thu, Apr 13, 2017 at 5:30 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 4/13/17 7:59 AM, Anshul Lahariya wrote:
>>>
>>> Now i perform a new md, there is a problem with this error
>>>>
>>>>
>>>> [anshu at dhcppc58 AhpE_MSH]$ gmx mdrun -v -deffnm md_1_0
>>>> :-) 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 -deffnm md_1_0
>>>>
>>>>
>>>> NOTE: Error occurred during GPU detection:
>>>> OpenCL error -1001
>>>> Can not use GPU acceleration, will fall back to CPU kernels.
>>>>
>>>>
>>>> Running on 1 node with total 2 cores, 4 logical cores, 0 compatible GPUs
>>>> Hardware detected:
>>>> CPU info:
>>>> Vendor: Intel
>>>> Brand: Intel(R) Core(TM) i7-6500U CPU @ 2.50GHz
>>>> SIMD instructions most likely to fit this hardware: AVX2_256
>>>> SIMD instructions selected at GROMACS compile time: SSE2
>>>>
>>>> Hardware topology: Full, with devices
>>>>
>>>> Compiled SIMD instructions: SSE2, GROMACS could use AVX2_256 on this
>>>> machine, which is better.
>>>>
>>>> Reading file md_1_0.tpr, VERSION 2016.2 (single precision)
>>>> Changing nstlist from 10 to 25, rlist from 1.4 to 1.431
>>>>
>>>> Using 1 MPI thread
>>>> Using 4 OpenMP threads
>>>>
>>>> starting mdrun 'Protein in water'
>>>> 5000000 steps, 10000.0 ps.
>>>> step 40800, will finish Sun Apr 16 06:11:14 2017
>>>> Step 40875, time 81.75 (ps) LINCS WARNING
>>>> relative constraint deviation after LINCS:
>>>> rms 0.013405, max 0.537354 (between atoms 1541 and 1542)
>>>> bonds that rotated more than 30 degrees:
>>>> atom 1 atom 2 angle previous, current, constraint length
>>>> 1541 1542 90.0 0.1330 0.2045 0.1330
>>>>
>>>> step 40875: One or more water molecules can not be settled.
>>>> Check for bad contacts and/or reduce the timestep if appropriate.
>>>> Wrote pdb files with previous and current coordinates
>>>> Segmentation fault (core dumped)
>>>> [anshu at dhcppc58 AhpE_MSH]$
>>>>
>>>>
>>>>
>>>> Your system is unstable. Follow the link I posted before. It's
>>> impossible for anyone to diagnose anything based on this generic failure
>>> message.
>>>
>>> -Justin
>>>
>>>
>>>
>>>>
>>>>
>>>> On Thu, Apr 13, 2017 at 4:45 PM, Anshul Lahariya <
>>>> anshullahariya17 at gmail.com
>>>>
>>>> wrote:
>>>>>
>>>>>
>>>> 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....
>>>>>>>>>>>>>> --
>>>>>>>>>>>>>> Gromacs Users mailing list
>>>>>>>>>>>>>>
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>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Gromacs Users mailing list
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>>>>>>>>>>>>> /Mailing_Lists/GMX-Users_List before posting!
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>>>>>>>>>>>>>
>>>>>>>>>>>>> or
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>> --
>>>>>>>>>>>>
>>>>>>>>>>>> Gromacs Users mailing list
>>>>>>>>>>>
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>>>>>>>>>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>>>>>>>>>
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>>>>>>>>>>> -users
>>>>>>>>>>> or
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>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>>
>>>>>>>>>>> Gromacs Users mailing list
>>>>>>>>>>
>>>>>>>>>> * Please search the archive at http://www.gromacs.org/Support
>>>>>>>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>>>>>>>
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>>>>>>>>>> -users
>>>>>>>>>> or
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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
>>>>>>
>>>>>> ==================================================
>>>>>>
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
>>>>>> * Please search the archive at http://www.gromacs.org/Support
>>>>>> /Mailing_Lists/GMX-Users_List before posting!
>>>>>>
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>>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>> --
>>> ==================================================
>>>
>>> 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
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
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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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