[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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>>>>>>>>>>>>>>
>>>>>>>>>>>>>> -users or
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> --
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> Gromacs Users mailing list
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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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>>>>>>>>>> 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!
>>>>>>
>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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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
>>>
>>> ==================================================
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>>> 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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