[gmx-users] need you help - New user

[Urszula Uciechowska]

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/