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 <jalem...@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@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@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 <
anshullahariy...@gmail.com
wrote:
okkk,,, thank u justin sir
On Thu, Apr 13, 2017 at 3:51 PM, Justin Lemkul <jalem...@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@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 <
anshullahariy...@gmail.com
wrote:
thankss tasneem.
let me try.
On Thu, Apr 13, 2017 at 3:40 PM, Anshul Lahariya <
anshullahariy...@gmail.com> wrote:
powercut take place and md stops, so i want to continue my md
[root@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@dhcppc58 AhpE_MSH]# ^C
[root@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 <
tasneemkausa...@gmail.com> wrote:
please give the exact command and error message.
On Thu, Apr 13, 2017 at 3:30 PM, Anshul Lahariya <
anshullahariy...@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 <
anshullahariy...@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 <zebami...@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 <
anshullahariy...@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@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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/Mailing_Lists/GMX-Users_List before posting!
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send a mail to gmx-users-requ...@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
Gromacs Users mailing list
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send a mail to gmx-users-requ...@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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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