[gmx-users] need you help - New user
Justin Lemkul
jalemkul at vt.edu
Mon Jun 2 14:07:11 CEST 2014
On 6/2/14, 7:47 AM, Urszula Uciechowska wrote:
> It is still not there. I have also tried to use command:
>
> $MDRUN -v -s nvt.tpr -o nvt.trr -x nvt.xtc -c nvt.gro -g nvt.log -e nvt
> nvt.edr
>
> I am using gromacs/4.5.3-s.
>
> Before sumbitting NVT I run simple energy min.
>
> I attached my NVT.mdp file...
>
The list does not accept attachments. If you want to post your .mdp file,
please simply copy and paste its contents into an email.
> I do not know what is wrong..
>
Your .log file indicates that the run finished; can you verify using gmxcheck
that your energy and trajectory files contain all the expected frames? Based on
the very poor performance in the .log file, I would expect either (1) your
system is enormous or (2) your hardware is simply performing badly. If the
former, do you have sufficient disk space to be writing the output? It is
possible that your disk is simply filling up before the final coordinate file
can be written, though the .log file should print an error message if that's the
case.
-Justin
> Please suggest me something
> /Urszula
>
>
>> Try using the following command
>>
>> mdrun -v -deffnm nvt
>>
>>
>> On Mon, Jun 2, 2014 at 11:23 AM, Urszula Uciechowska <
>> urszula.uciechowska at biotech.ug.edu.pl> wrote:
>>
>>> Dear Gromacs users,
>>>
>>> I am having problem running NVT calculation, when is finished I do not
>>> see
>>> the *.gro file among the out file. I do not know what the problem can
>>> be.
>>> I am not getting any error.
>>>
>>> The command that I used:
>>>
>>> mdrun -s input_nvt.tpr -deffnm nvt -v
>>>
>>> in .Log file I have
>>>
>>> R E A L C Y C L E A N D T I M E A C C O U N T I N G
>>>
>>> Computing: Nodes Number G-Cycles Seconds %
>>> -----------------------------------------------------------------------
>>> Domain decomp. 6 770 1779.164 785.2 5.5
>>> DD comm. load 6 769 10.582 4.7 0.0
>>> DD comm. bounds 6 769 11.246 5.0 0.0
>>> Send X to PME 6 770 37.780 16.7 0.1
>>> Comm. coord. 6 770 71.593 31.6 0.2
>>> Neighbor search 6 770 5301.193 2339.7 16.5
>>> Force 6 770 5327.504 2351.3 16.6
>>> Wait + Comm. F 6 770 1984.758 876.0 6.2
>>> PME mesh 6 770 5970.668 2635.1 18.6
>>> Wait + Comm. X/F 6 10102.647 4458.8 31.4
>>> Wait + Recv. PME F 6 770 36.705 16.2 0.1
>>> Write traj. 6 10 21.644 9.6 0.1
>>> Update 6 770 205.313 90.6 0.6
>>> Constraints 6 770 778.976 343.8 2.4
>>> Comm. energies 6 771 301.011 132.9 0.9
>>> Rest 6 208.397 92.0 0.6
>>> -----------------------------------------------------------------------
>>> Total 12 32149.180 14189.0 100.0
>>> -----------------------------------------------------------------------
>>> -----------------------------------------------------------------------
>>> PME redist. X/F 6 1540 565.866 249.7 1.8
>>> PME spread/gather 6 1540 2972.849 1312.1 9.2
>>> PME 3D-FFT 6 1540 1841.695 812.8 5.7
>>> PME solve 6 770 590.096 260.4 1.8
>>> -----------------------------------------------------------------------
>>>
>>> Parallel run - timing based on wallclock.
>>>
>>> NODE (s) Real (s) (%)
>>> Time: 1182.415 1182.415 100.0
>>> 19:42
>>> (Mnbf/s) (GFlops) (ns/day) (hour/ns)
>>> Performance: 129.307 11.117 0.113 213.278
>>> Finished mdrun on node 0 Mon Jun 2 11:00:09 2014
>>> (END)
>>>
>>>
>>> Thank you for your help.
>>>
>>> Urszula Uciechowska
>>>
>>>
>>> -----------------------------------------
>>> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
>>> http://www.ug.edu.pl/
>>>
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>
>
>
> -----------------------------------------
> Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
> http://www.ug.edu.pl/
>
>
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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