[gmx-users] need you help - New user

[MUSYOKA THOMMAS]

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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