[gmx-users] need you help - New user
Urszula Uciechowska
urszula.uciechowska at biotech.ug.edu.pl
Mon Jun 2 13:58:14 CEST 2014
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...
I do not know what is wrong..
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
>>
>>
>> -----------------------------------------
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>> http://www.ug.edu.pl/
>>
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